Starting phenix.real_space_refine on Sat Mar 7 10:47:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zi4_14737/03_2026/7zi4_14737.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zi4_14737/03_2026/7zi4_14737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zi4_14737/03_2026/7zi4_14737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zi4_14737/03_2026/7zi4_14737.map" model { file = "/net/cci-nas-00/data/ceres_data/7zi4_14737/03_2026/7zi4_14737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zi4_14737/03_2026/7zi4_14737.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 1.133 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 331 5.49 5 S 158 5.16 5 Be 1 3.05 5 C 25618 2.51 5 N 7565 2.21 5 O 8617 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42294 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3323 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3261 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3394 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3356 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 427} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3402 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3335 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 4962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 4962 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 28, 'TRANS': 653} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 816 Unresolved non-hydrogen dihedrals: 530 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 15, 'ASN:plan1': 14, 'GLU:plan': 23, 'ARG:plan': 16, 'TRP:plan': 1, 'PHE:plan': 3, 'HIS:plan': 5, 'ASP:plan': 15, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 378 Chain: "N" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 758 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3109 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 29, 'TRANS': 382} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "Q" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 735 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 5, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "I" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 751 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 747 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: "O" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 839 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3223 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "Y" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3252 Classifications: {'DNA': 158} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 157} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26163 SG CYS R 309 13.916 62.361 140.805 1.00142.09 S ATOM 26193 SG CYS R 314 13.612 63.046 144.568 1.00143.88 S ATOM 26312 SG CYS R 330 17.008 62.330 143.328 1.00133.28 S ATOM 26341 SG CYS R 334 14.621 59.563 143.201 1.00136.57 S Time building chain proxies: 9.36, per 1000 atoms: 0.22 Number of scatterers: 42294 At special positions: 0 Unit cell: (134.2, 189.2, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 158 16.00 P 331 15.00 F 3 9.00 O 8617 8.00 N 7565 7.00 C 25618 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 401 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 334 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 330 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 314 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 309 " Number of angles added : 6 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8708 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 44 sheets defined 49.4% alpha, 10.5% beta 146 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 5.85 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.751A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.621A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.637A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.693A pdb=" N LEU A 263 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.762A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.663A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 320 " --> pdb=" O HIS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.817A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.300A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.633A pdb=" N LYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.517A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.613A pdb=" N ASP A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 454 removed outlier: 3.616A pdb=" N TYR A 454 " --> pdb=" O GLN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'B' and resid 49 through 66 removed outlier: 3.702A pdb=" N ARG B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.831A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.620A pdb=" N LEU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.972A pdb=" N ASP B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.602A pdb=" N SER B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 286 removed outlier: 3.646A pdb=" N ARG B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 316 removed outlier: 3.575A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.986A pdb=" N ARG B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 379 Processing helix chain 'B' and resid 384 through 397 removed outlier: 4.293A pdb=" N THR B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 416 removed outlier: 3.784A pdb=" N ILE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.600A pdb=" N ARG B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 445 removed outlier: 4.282A pdb=" N GLU B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.712A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.506A pdb=" N GLY C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.573A pdb=" N VAL C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 3.514A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 262 removed outlier: 3.631A pdb=" N MET C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.672A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.694A pdb=" N TYR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.610A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.749A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 420 removed outlier: 3.646A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 441 through 450 removed outlier: 3.698A pdb=" N GLN C 450 " --> pdb=" O ILE C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.627A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.764A pdb=" N SER D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.938A pdb=" N ARG D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.651A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.593A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 379 removed outlier: 3.563A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.604A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 444 Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.942A pdb=" N LYS E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.114A pdb=" N GLU E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.679A pdb=" N LEU E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 removed outlier: 3.543A pdb=" N MET E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 289 removed outlier: 3.916A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.875A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU E 320 " --> pdb=" O HIS E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 367 through 383 Processing helix chain 'E' and resid 387 through 402 removed outlier: 3.788A pdb=" N HIS E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 409 removed outlier: 3.574A pdb=" N SER E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU E 409 " --> pdb=" O TYR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 421 Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 450 Processing helix chain 'E' and resid 451 through 454 removed outlier: 3.694A pdb=" N TYR E 454 " --> pdb=" O GLN E 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 451 through 454' Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.733A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.734A pdb=" N ALA F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.104A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.651A pdb=" N LEU F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.832A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.634A pdb=" N MET F 303 " --> pdb=" O GLU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.695A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 removed outlier: 3.897A pdb=" N ILE F 373 " --> pdb=" O GLN F 369 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.558A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 removed outlier: 3.582A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR F 446 " --> pdb=" O TYR F 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 536 Processing helix chain 'G' and resid 548 through 560 removed outlier: 3.651A pdb=" N LEU G 560 " --> pdb=" O LEU G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 578 through 590 removed outlier: 3.862A pdb=" N VAL G 590 " --> pdb=" O PHE G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.778A pdb=" N TRP G 612 " --> pdb=" O ILE G 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 630 through 637 Processing helix chain 'G' and resid 637 through 643 removed outlier: 3.504A pdb=" N PHE G 641 " --> pdb=" O ASP G 637 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 657 removed outlier: 3.935A pdb=" N ALA G 656 " --> pdb=" O GLU G 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 670 removed outlier: 3.621A pdb=" N LYS G 666 " --> pdb=" O SER G 662 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.712A pdb=" N LEU G 691 " --> pdb=" O THR G 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 712 Processing helix chain 'G' and resid 730 through 740 Processing helix chain 'G' and resid 768 through 780 Processing helix chain 'G' and resid 809 through 818 Processing helix chain 'G' and resid 841 through 848 Processing helix chain 'G' and resid 849 through 854 Processing helix chain 'G' and resid 854 through 864 removed outlier: 4.182A pdb=" N TRP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) Processing helix chain 'G' and resid 868 through 878 Processing helix chain 'G' and resid 889 through 894 removed outlier: 3.855A pdb=" N PHE G 893 " --> pdb=" O SER G 889 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 907 removed outlier: 3.680A pdb=" N ALA G 902 " --> pdb=" O PRO G 898 " (cutoff:3.500A) Processing helix chain 'G' and resid 908 through 933 removed outlier: 4.921A pdb=" N TYR G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG G 925 " --> pdb=" O LYS G 921 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY G 933 " --> pdb=" O LEU G 929 " (cutoff:3.500A) Processing helix chain 'G' and resid 958 through 965 Processing helix chain 'G' and resid 965 through 972 removed outlier: 3.699A pdb=" N LYS G 969 " --> pdb=" O CYS G 965 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER G 970 " --> pdb=" O PRO G 966 " (cutoff:3.500A) Processing helix chain 'G' and resid 1007 through 1011 removed outlier: 3.568A pdb=" N LEU G1010 " --> pdb=" O PRO G1007 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1039 Processing helix chain 'G' and resid 1043 through 1053 Processing helix chain 'G' and resid 1054 through 1064 Processing helix chain 'G' and resid 1065 through 1067 No H-bonds generated for 'chain 'G' and resid 1065 through 1067' Processing helix chain 'G' and resid 1094 through 1100 removed outlier: 3.714A pdb=" N THR G1098 " --> pdb=" O GLU G1094 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER G1100 " --> pdb=" O LEU G1096 " (cutoff:3.500A) Processing helix chain 'G' and resid 1100 through 1117 Processing helix chain 'G' and resid 1126 through 1140 Processing helix chain 'G' and resid 1152 through 1164 removed outlier: 3.681A pdb=" N GLN G1164 " --> pdb=" O VAL G1160 " (cutoff:3.500A) Processing helix chain 'G' and resid 1176 through 1180 Processing helix chain 'G' and resid 1202 through 1211 removed outlier: 3.803A pdb=" N ALA G1206 " --> pdb=" O VAL G1202 " (cutoff:3.500A) Processing helix chain 'G' and resid 1230 through 1249 removed outlier: 3.905A pdb=" N ILE G1234 " --> pdb=" O ILE G1230 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE G1249 " --> pdb=" O GLN G1245 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 29 Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU N 63 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL N 65 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE N 66 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 94 removed outlier: 4.019A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 28 Processing helix chain 'R' and resid 331 through 342 Processing helix chain 'H' and resid 106 through 120 Processing helix chain 'H' and resid 143 through 157 removed outlier: 4.090A pdb=" N CYS H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 175 Processing helix chain 'H' and resid 214 through 230 Processing helix chain 'H' and resid 238 through 249 Processing helix chain 'H' and resid 255 through 263 Processing helix chain 'H' and resid 265 through 270 removed outlier: 3.798A pdb=" N GLU H 270 " --> pdb=" O PRO H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 451 Processing helix chain 'H' and resid 452 through 455 removed outlier: 3.912A pdb=" N ILE H 455 " --> pdb=" O PRO H 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 452 through 455' Processing helix chain 'H' and resid 457 through 461 Processing helix chain 'H' and resid 467 through 477 removed outlier: 3.737A pdb=" N LEU H 472 " --> pdb=" O ILE H 468 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN H 473 " --> pdb=" O ALA H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 489 removed outlier: 3.753A pdb=" N GLU H 485 " --> pdb=" O LYS H 481 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET H 486 " --> pdb=" O ASP H 482 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 487 " --> pdb=" O ILE H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 515 removed outlier: 3.539A pdb=" N MET H 514 " --> pdb=" O GLU H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 543 Processing helix chain 'H' and resid 555 through 560 removed outlier: 3.595A pdb=" N GLU H 559 " --> pdb=" O LYS H 555 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 152 Processing helix chain 'Q' and resid 199 through 209 Processing helix chain 'Q' and resid 210 through 221 removed outlier: 3.600A pdb=" N VAL Q 214 " --> pdb=" O PRO Q 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG Q 221 " --> pdb=" O TYR Q 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 55 Processing helix chain 'I' and resid 63 through 79 removed outlier: 4.130A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 Processing helix chain 'I' and resid 120 through 132 removed outlier: 3.536A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 63 removed outlier: 3.673A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 76 Processing helix chain 'J' and resid 82 through 93 removed outlier: 3.582A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.500A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU K 65 " --> pdb=" O GLU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'K' and resid 112 through 116 Processing helix chain 'L' and resid 37 through 49 Processing helix chain 'L' and resid 55 through 84 removed outlier: 3.752A pdb=" N ARG L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS L 82 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.925A pdb=" N THR L 96 " --> pdb=" O ARG L 92 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG L 99 " --> pdb=" O GLN L 95 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU L 102 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 123 Processing helix chain 'M' and resid 44 through 55 Processing helix chain 'M' and resid 63 through 79 Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 132 removed outlier: 3.735A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 46 through 72 removed outlier: 3.601A pdb=" N ASP O 72 " --> pdb=" O ASN O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 89 Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 37 through 49 removed outlier: 3.997A pdb=" N LYS P 43 " --> pdb=" O ILE P 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS P 46 " --> pdb=" O TYR P 42 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLN P 47 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL P 48 " --> pdb=" O VAL P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 84 Processing helix chain 'P' and resid 90 through 102 Processing helix chain 'P' and resid 104 through 123 removed outlier: 3.800A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.399A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 359 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 140 removed outlier: 6.419A pdb=" N GLY A 160 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 138 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 158 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 166 " --> pdb=" O THR A 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 172 current: chain 'A' and resid 200 through 206 removed outlier: 5.468A pdb=" N VAL A 221 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.659A pdb=" N CYS A 336 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.756A pdb=" N SER B 43 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 104 removed outlier: 3.530A pdb=" N ALA B 327 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 71 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET B 326 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 73 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR B 328 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE B 75 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 72 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL B 357 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 74 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 147 removed outlier: 6.720A pdb=" N THR B 162 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE B 145 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS B 160 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 159 " --> pdb=" O LEU B 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 174 current: chain 'B' and resid 202 through 207 Processing sheet with id=AA8, first strand: chain 'B' and resid 333 through 334 Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.280A pdb=" N ILE C 3 " --> pdb=" O LEU G 762 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR G 764 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU C 5 " --> pdb=" O TYR G 764 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE G1193 " --> pdb=" O TYR G1222 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU G1121 " --> pdb=" O ILE G1192 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL G1120 " --> pdb=" O PHE G1172 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU G1174 " --> pdb=" O VAL G1120 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE G1122 " --> pdb=" O LEU G1174 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET G1145 " --> pdb=" O LEU G1173 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N SER G1175 " --> pdb=" O MET G1145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.319A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 142 removed outlier: 6.428A pdb=" N GLY C 160 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 138 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 158 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS C 156 " --> pdb=" O PRO C 140 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU C 142 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 154 " --> pdb=" O GLU C 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 172 current: chain 'C' and resid 200 through 206 removed outlier: 4.801A pdb=" N VAL C 221 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG C 205 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.540A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL D 73 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR D 328 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE D 75 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 150 removed outlier: 5.442A pdb=" N VAL D 142 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS D 164 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU D 144 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 158 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 174 current: chain 'D' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 202 through 207 current: chain 'E' and resid 152 through 154 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 152 through 154 current: chain 'G' and resid 996 through 998 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 996 through 998 current: chain 'R' and resid 282 through 286 Processing sheet with id=AB8, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB9, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 97 removed outlier: 6.539A pdb=" N CYS E 94 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP E 302 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET E 96 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA E 330 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 301 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 120 through 139 removed outlier: 5.566A pdb=" N VAL E 135 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS E 162 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU E 137 " --> pdb=" O GLY E 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 172 current: chain 'E' and resid 200 through 205 Processing sheet with id=AC3, first strand: chain 'E' and resid 335 through 337 Processing sheet with id=AC4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'F' and resid 100 through 104 removed outlier: 3.585A pdb=" N ALA F 327 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 128 through 147 removed outlier: 5.476A pdb=" N VAL F 142 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS F 164 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 144 " --> pdb=" O THR F 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 172 current: chain 'F' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 202 through 207 current: chain 'R' and resid 328 through 329 Processing sheet with id=AC7, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AC8, first strand: chain 'G' and resid 626 through 629 removed outlier: 6.631A pdb=" N PHE G 570 " --> pdb=" O VAL G 627 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR G 629 " --> pdb=" O PHE G 570 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE G 572 " --> pdb=" O THR G 629 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU G 571 " --> pdb=" O VAL G 650 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET G 649 " --> pdb=" O LEU G 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 831 through 833 Processing sheet with id=AD1, first strand: chain 'G' and resid 838 through 839 removed outlier: 6.244A pdb=" N TYR G 838 " --> pdb=" O TYR G1025 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 980 through 984 removed outlier: 6.896A pdb=" N THR G1004 " --> pdb=" O SER G 981 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR G 983 " --> pdb=" O LEU G1002 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU G1002 " --> pdb=" O TYR G 983 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 45 through 46 removed outlier: 7.783A pdb=" N ARG N 45 " --> pdb=" O ILE M 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 80 through 81 Processing sheet with id=AD5, first strand: chain 'N' and resid 96 through 98 removed outlier: 6.568A pdb=" N THR N 96 " --> pdb=" O THR K 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.505A pdb=" N GLY H 45 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE H 61 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA H 44 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU H 59 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AD8, first strand: chain 'H' and resid 98 through 99 removed outlier: 3.600A pdb=" N VAL H 102 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AE1, first strand: chain 'H' and resid 209 through 211 removed outlier: 3.711A pdb=" N LYS H 209 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU H 184 " --> pdb=" O PHE H 492 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR H 494 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE H 186 " --> pdb=" O THR H 494 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL H 491 " --> pdb=" O GLN H 524 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 83 through 84 removed outlier: 6.757A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AE4, first strand: chain 'J' and resid 96 through 98 Processing sheet with id=AE5, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.635A pdb=" N ARG K 42 " --> pdb=" O ILE L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 77 through 78 removed outlier: 3.517A pdb=" N ILE K 78 " --> pdb=" O GLY L 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.840A pdb=" N ARG O 42 " --> pdb=" O ILE P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'O' and resid 77 through 78 1523 hydrogen bonds defined for protein. 4440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 11.96 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10722 1.33 - 1.45: 9220 1.45 - 1.57: 22795 1.57 - 1.69: 655 1.69 - 1.81: 262 Bond restraints: 43654 Sorted by residual: bond pdb=" F2 BEF G1602 " pdb="BE BEF G1602 " ideal model delta sigma weight residual 1.476 1.708 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" F1 BEF G1602 " pdb="BE BEF G1602 " ideal model delta sigma weight residual 1.476 1.703 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" F3 BEF G1602 " pdb="BE BEF G1602 " ideal model delta sigma weight residual 1.476 1.688 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" N MET E 147 " pdb=" CA MET E 147 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.15e-02 7.56e+03 9.20e+00 bond pdb=" CA SER P 36 " pdb=" CB SER P 36 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.69e-02 3.50e+03 6.24e+00 ... (remaining 43649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 60293 4.26 - 8.51: 153 8.51 - 12.77: 1 12.77 - 17.03: 1 17.03 - 21.28: 1 Bond angle restraints: 60449 Sorted by residual: angle pdb=" F1 BEF G1602 " pdb="BE BEF G1602 " pdb=" F3 BEF G1602 " ideal model delta sigma weight residual 120.12 98.84 21.28 3.00e+00 1.11e-01 5.03e+01 angle pdb=" C3' DC X -70 " pdb=" O3' DC X -70 " pdb=" P DT X -69 " ideal model delta sigma weight residual 120.20 112.03 8.17 1.50e+00 4.44e-01 2.96e+01 angle pdb=" F2 BEF G1602 " pdb="BE BEF G1602 " pdb=" F3 BEF G1602 " ideal model delta sigma weight residual 119.96 105.16 14.80 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N TYR P 37 " pdb=" CA TYR P 37 " pdb=" C TYR P 37 " ideal model delta sigma weight residual 112.88 106.69 6.19 1.29e+00 6.01e-01 2.30e+01 angle pdb=" C PHE G 822 " pdb=" N GLU G 823 " pdb=" CA GLU G 823 " ideal model delta sigma weight residual 122.92 115.04 7.88 1.75e+00 3.27e-01 2.03e+01 ... (remaining 60444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 23969 35.42 - 70.84: 1620 70.84 - 106.27: 45 106.27 - 141.69: 4 141.69 - 177.11: 6 Dihedral angle restraints: 25644 sinusoidal: 12144 harmonic: 13500 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 128.73 171.27 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 130.02 169.99 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 130.27 169.73 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 25641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 6707 0.100 - 0.200: 247 0.200 - 0.299: 1 0.299 - 0.399: 0 0.399 - 0.499: 3 Chirality restraints: 6958 Sorted by residual: chirality pdb=" P DC X -70 " pdb=" OP1 DC X -70 " pdb=" OP2 DC X -70 " pdb=" O5' DC X -70 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" P DT X -69 " pdb=" OP1 DT X -69 " pdb=" OP2 DT X -69 " pdb=" O5' DT X -69 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" P DC X -68 " pdb=" OP1 DC X -68 " pdb=" OP2 DC X -68 " pdb=" O5' DC X -68 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 6955 not shown) Planarity restraints: 6640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 590 " -0.087 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO G 591 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO G 591 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO G 591 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 575 " -0.070 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO H 576 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO H 576 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO H 576 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 109 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR E 109 " -0.071 2.00e-02 2.50e+03 pdb=" O THR E 109 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU E 110 " 0.024 2.00e-02 2.50e+03 ... (remaining 6637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 676 2.66 - 3.22: 38609 3.22 - 3.78: 67679 3.78 - 4.34: 90098 4.34 - 4.90: 140744 Nonbonded interactions: 337806 Sorted by model distance: nonbonded pdb=" O2 DC X -30 " pdb=" N2 DG Y 30 " model vdw 2.100 2.496 nonbonded pdb=" O3B ADP G1601 " pdb="BE BEF G1602 " model vdw 2.115 2.420 nonbonded pdb=" OH TYR B 401 " pdb=" O PHE B 433 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR P 90 " pdb=" OE1 GLU P 93 " model vdw 2.166 3.040 nonbonded pdb=" O2 DC X -43 " pdb=" N2 DG Y 43 " model vdw 2.167 2.496 ... (remaining 337801 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 12 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 141 or (resid 152 through 153 and \ (name N or name CA or name C or name O or name CB )) or resid 154 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 through 184 or (resid 185 and (name N or name CA or name C or name O or name C \ B )) or resid 186 through 284 or (resid 285 and (name N or name CA or name C or \ name O or name CB )) or resid 286 through 345 or (resid 346 and (name N or name \ CA or name C or name O or name CB )) or resid 347 through 438 or (resid 439 thro \ ugh 440 and (name N or name CA or name C or name O or name CB )) or resid 441 or \ (resid 442 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 3 through 452 or (resid 453 and (name N or name CA or name C or name O or name C \ B )) or resid 454 through 501)) selection = (chain 'C' and (resid 12 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 141 or resid 152 through 184 or (r \ esid 185 and (name N or name CA or name C or name O or name CB )) or resid 186 t \ hrough 231 or (resid 232 and (name N or name CA or name C or name O or name CB ) \ ) or resid 233 through 253 or (resid 254 through 257 and (name N or name CA or n \ ame C or name O or name CB )) or resid 258 through 302 or (resid 303 and (name N \ or name CA or name C or name O or name CB )) or resid 304 through 441 or (resid \ 442 and (name N or name CA or name C or name O or name CB )) or resid 443 throu \ gh 501)) selection = (chain 'E' and (resid 12 through 141 or (resid 152 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )) or resid 158 through 231 \ or (resid 232 and (name N or name CA or name C or name O or name CB )) or resid \ 233 through 253 or (resid 254 through 257 and (name N or name CA or name C or n \ ame O or name CB )) or resid 258 through 284 or (resid 285 and (name N or name C \ A or name C or name O or name CB )) or resid 286 through 302 or (resid 303 and ( \ name N or name CA or name C or name O or name CB )) or resid 304 through 345 or \ (resid 346 and (name N or name CA or name C or name O or name CB )) or resid 347 \ through 438 or (resid 439 through 440 and (name N or name CA or name C or name \ O or name CB )) or resid 441 through 452 or (resid 453 and (name N or name CA or \ name C or name O or name CB )) or resid 454 through 501)) } ncs_group { reference = (chain 'B' and (resid 15 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161 through 168 or (resid 169 \ and (name N or name CA or name C or name O or name CB )) or resid 170 through 20 \ 8 or (resid 209 and (name N or name CA or name C or name O or name CB )) or resi \ d 210 through 245 or (resid 246 and (name N or name CA or name C or name O or na \ me CB )) or resid 247 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 363 or (resid 364 and (name N or n \ ame CA or name C or name O or name CB )) or resid 365 through 426 or (resid 427 \ and (name N or name CA or name C or name O or name CB )) or resid 428 through 44 \ 3 or (resid 444 through 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 through 501)) selection = (chain 'D' and (resid 15 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 or (resid 63 and (name N or n \ ame CA or name C or name O or name CB )) or resid 64 through 66 or (resid 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 148 or \ (resid 149 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 56 through 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 159 or (resid 160 and (name N or name CA or name C or name O or nam \ e CB )) or resid 161 through 168 or (resid 169 and (name N or name CA or name C \ or name O or name CB )) or resid 170 through 214 or resid 222 through 245 or (re \ sid 246 and (name N or name CA or name C or name O or name CB )) or resid 247 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 391 or (resid 392 and (name N or name CA or name C or name \ O or name CB )) or resid 393 through 395 or (resid 396 and (name N or name CA o \ r name C or name O or name CB )) or resid 397 through 443 or (resid 444 through \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 throug \ h 501)) selection = (chain 'F' and (resid 15 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 through 66 or (resid 67 and ( \ name N or name CA or name C or name O or name CB )) or resid 68 through 149 or r \ esid 156 through 208 or (resid 209 and (name N or name CA or name C or name O or \ name CB )) or resid 210 or (resid 211 through 214 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 222 through 223 and (name N or name CA or \ name C or name O or name CB )) or resid 224 through 278 or (resid 279 and (name \ N or name CA or name C or name O or name CB )) or resid 280 through 348 or (resi \ d 349 and (name N or name CA or name C or name O or name CB )) or resid 350 thro \ ugh 363 or (resid 364 and (name N or name CA or name C or name O or name CB )) o \ r resid 365 through 391 or (resid 392 and (name N or name CA or name C or name O \ or name CB )) or resid 393 through 395 or (resid 396 and (name N or name CA or \ name C or name O or name CB )) or resid 397 through 426 or (resid 427 and (name \ N or name CA or name C or name O or name CB )) or resid 428 through 501)) } ncs_group { reference = (chain 'I' and (resid 43 through 133 or (resid 134 through 135 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 43 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 135)) } ncs_group { reference = (chain 'J' and resid 24 through 102) selection = (chain 'N' and (resid 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O )))) } ncs_group { reference = (chain 'K' and ((resid 13 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 117 or (resid 118 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'O' and resid 13 through 118) } ncs_group { reference = (chain 'L' and (resid 31 through 115 or (resid 116 through 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 123)) selection = (chain 'P' and (resid 31 through 119 or (resid 120 and (name N or name CA or nam \ e C or name O or name CB )) or resid 121 through 123)) } 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 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: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 49.820 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.849 43659 Z= 0.436 Angle : 0.614 21.282 60455 Z= 0.321 Chirality : 0.041 0.499 6958 Planarity : 0.005 0.135 6640 Dihedral : 19.742 177.109 16936 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.95 % Favored : 94.83 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.12), residues: 4626 helix: 0.31 (0.12), residues: 2155 sheet: -0.33 (0.20), residues: 643 loop : -1.37 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 208 TYR 0.029 0.001 TYR G1144 PHE 0.031 0.001 PHE G 853 TRP 0.030 0.002 TRP G 712 HIS 0.005 0.001 HIS R 27 Details of bonding type rmsd covalent geometry : bond 0.00323 (43654) covalent geometry : angle 0.61205 (60449) hydrogen bonds : bond 0.14008 ( 1894) hydrogen bonds : angle 5.30053 ( 5170) metal coordination : bond 0.00422 ( 4) metal coordination : angle 4.88117 ( 6) Misc. bond : bond 0.84851 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 448 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.6656 (mmt) cc_final: 0.6388 (mmt) REVERT: C 278 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 274 GLU cc_start: 0.7646 (mp0) cc_final: 0.7443 (mp0) REVERT: F 213 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7988 (tpp80) REVERT: G 559 HIS cc_start: 0.6199 (m170) cc_final: 0.5965 (t70) REVERT: R 327 GLN cc_start: 0.7266 (mp10) cc_final: 0.6836 (mp10) REVERT: H 46 TRP cc_start: 0.7399 (m100) cc_final: 0.7154 (m-10) REVERT: H 242 MET cc_start: 0.8224 (mmp) cc_final: 0.8019 (mmp) REVERT: H 504 LYS cc_start: 0.7227 (tttt) cc_final: 0.6914 (ttpp) REVERT: H 555 LYS cc_start: 0.9194 (tmmt) cc_final: 0.8980 (tptt) REVERT: Q 206 ILE cc_start: 0.8979 (tt) cc_final: 0.8745 (pt) REVERT: I 80 THR cc_start: 0.8460 (p) cc_final: 0.8122 (p) REVERT: J 27 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8079 (mm-40) REVERT: L 37 TYR cc_start: 0.8498 (m-80) cc_final: 0.8286 (m-80) outliers start: 8 outliers final: 3 residues processed: 455 average time/residue: 0.2397 time to fit residues: 184.5299 Evaluate side-chains 364 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 361 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain P residue 36 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** G 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 GLN ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.089981 restraints weight = 88396.191| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.59 r_work: 0.3224 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 43659 Z= 0.282 Angle : 0.704 11.061 60455 Z= 0.368 Chirality : 0.045 0.226 6958 Planarity : 0.005 0.079 6640 Dihedral : 21.854 168.636 8622 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 1.62 % Allowed : 9.21 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.12), residues: 4626 helix: 0.30 (0.11), residues: 2192 sheet: -0.53 (0.19), residues: 672 loop : -1.56 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 362 TYR 0.024 0.002 TYR G1136 PHE 0.033 0.002 PHE G 853 TRP 0.027 0.002 TRP G 712 HIS 0.007 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00663 (43654) covalent geometry : angle 0.70010 (60449) hydrogen bonds : bond 0.05811 ( 1894) hydrogen bonds : angle 4.39388 ( 5170) metal coordination : bond 0.01046 ( 4) metal coordination : angle 7.28236 ( 6) Misc. bond : bond 0.00530 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 260 MET cc_start: 0.7857 (ttp) cc_final: 0.7459 (ttp) REVERT: C 278 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8141 (tm-30) REVERT: D 144 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6778 (pm20) REVERT: E 28 GLU cc_start: 0.8240 (tp30) cc_final: 0.8026 (tp30) REVERT: E 260 MET cc_start: 0.8839 (mmt) cc_final: 0.8622 (mmt) REVERT: F 213 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8144 (tpp80) REVERT: F 326 MET cc_start: 0.8788 (mtt) cc_final: 0.8530 (mtt) REVERT: F 443 MET cc_start: 0.6756 (ttt) cc_final: 0.6540 (ttt) REVERT: G 559 HIS cc_start: 0.6382 (m170) cc_final: 0.6146 (t70) REVERT: G 775 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: G 1129 MET cc_start: 0.7658 (mmm) cc_final: 0.7458 (tpp) REVERT: H 46 TRP cc_start: 0.7546 (m100) cc_final: 0.7233 (m100) REVERT: H 110 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7862 (mt-10) REVERT: H 504 LYS cc_start: 0.7431 (tttt) cc_final: 0.7057 (ttpp) REVERT: H 555 LYS cc_start: 0.9385 (tmmt) cc_final: 0.9147 (tptt) REVERT: Q 206 ILE cc_start: 0.8848 (tt) cc_final: 0.8567 (pt) REVERT: J 24 ASP cc_start: 0.7529 (t70) cc_final: 0.6974 (t0) REVERT: L 37 TYR cc_start: 0.8948 (m-80) cc_final: 0.8575 (m-80) REVERT: L 108 LYS cc_start: 0.7859 (tppt) cc_final: 0.7587 (tppt) outliers start: 59 outliers final: 41 residues processed: 397 average time/residue: 0.2429 time to fit residues: 163.5730 Evaluate side-chains 371 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 550 THR Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 712 TRP Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain R residue 10 GLU Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain Q residue 181 VAL Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 252 optimal weight: 0.2980 chunk 230 optimal weight: 4.9990 chunk 485 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 305 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 398 optimal weight: 0.9990 chunk 395 optimal weight: 0.0970 chunk 202 optimal weight: 0.8980 chunk 274 optimal weight: 0.0370 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 408 GLN F 25 HIS G1142 HIS ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.124808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093678 restraints weight = 87371.508| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.67 r_work: 0.3440 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43659 Z= 0.115 Angle : 0.550 9.790 60455 Z= 0.288 Chirality : 0.039 0.204 6958 Planarity : 0.004 0.047 6640 Dihedral : 21.522 176.303 8621 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 1.43 % Allowed : 11.98 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4626 helix: 0.99 (0.11), residues: 2173 sheet: -0.39 (0.19), residues: 672 loop : -1.30 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 129 TYR 0.015 0.001 TYR O 57 PHE 0.024 0.001 PHE G 853 TRP 0.025 0.001 TRP G 712 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00251 (43654) covalent geometry : angle 0.54724 (60449) hydrogen bonds : bond 0.03864 ( 1894) hydrogen bonds : angle 3.79408 ( 5170) metal coordination : bond 0.00600 ( 4) metal coordination : angle 5.39460 ( 6) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 395 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8140 (pt) REVERT: B 378 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: D 144 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: D 168 MET cc_start: 0.7816 (mmm) cc_final: 0.7593 (mmm) REVERT: D 326 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8494 (mmm) REVERT: E 28 GLU cc_start: 0.8144 (tp30) cc_final: 0.7906 (tp30) REVERT: F 146 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7520 (tm-30) REVERT: G 559 HIS cc_start: 0.6451 (m170) cc_final: 0.6214 (t-90) REVERT: G 775 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: G 858 ASP cc_start: 0.7467 (t0) cc_final: 0.7029 (m-30) REVERT: G 1129 MET cc_start: 0.7807 (mmm) cc_final: 0.7600 (tpp) REVERT: N 58 LEU cc_start: 0.8683 (tp) cc_final: 0.8436 (tp) REVERT: R 11 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6171 (tm-30) REVERT: H 46 TRP cc_start: 0.7649 (m100) cc_final: 0.7318 (m100) REVERT: H 504 LYS cc_start: 0.7232 (tttt) cc_final: 0.6924 (ttpp) REVERT: H 555 LYS cc_start: 0.9364 (tmmt) cc_final: 0.9137 (tptt) REVERT: Q 206 ILE cc_start: 0.8894 (tt) cc_final: 0.8609 (pt) REVERT: I 80 THR cc_start: 0.8625 (p) cc_final: 0.8396 (p) REVERT: J 24 ASP cc_start: 0.7508 (t0) cc_final: 0.6997 (t0) REVERT: L 37 TYR cc_start: 0.8861 (m-80) cc_final: 0.8512 (m-80) REVERT: P 93 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6902 (mp0) outliers start: 52 outliers final: 26 residues processed: 432 average time/residue: 0.2519 time to fit residues: 185.2155 Evaluate side-chains 377 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 435 optimal weight: 5.9990 chunk 370 optimal weight: 0.0670 chunk 277 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 313 ASN H 473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.121948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092710 restraints weight = 88757.997| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.40 r_work: 0.3313 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 43659 Z= 0.231 Angle : 0.635 8.962 60455 Z= 0.332 Chirality : 0.042 0.225 6958 Planarity : 0.004 0.046 6640 Dihedral : 21.673 163.504 8621 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 2.56 % Allowed : 13.44 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4626 helix: 0.71 (0.11), residues: 2196 sheet: -0.46 (0.19), residues: 684 loop : -1.44 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 129 TYR 0.016 0.002 TYR J 51 PHE 0.030 0.002 PHE G 853 TRP 0.053 0.002 TRP G 712 HIS 0.004 0.001 HIS G 847 Details of bonding type rmsd covalent geometry : bond 0.00542 (43654) covalent geometry : angle 0.63227 (60449) hydrogen bonds : bond 0.05125 ( 1894) hydrogen bonds : angle 4.05958 ( 5170) metal coordination : bond 0.00845 ( 4) metal coordination : angle 6.30194 ( 6) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 341 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.6789 (mp10) REVERT: B 161 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8169 (pt) REVERT: B 378 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 214 ASP cc_start: 0.8360 (m-30) cc_final: 0.8120 (t0) REVERT: C 278 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 144 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: D 326 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8671 (mtm) REVERT: E 28 GLU cc_start: 0.8094 (tp30) cc_final: 0.7862 (tp30) REVERT: E 260 MET cc_start: 0.8562 (mmt) cc_final: 0.8271 (mmt) REVERT: F 213 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8216 (tpp80) REVERT: G 775 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: G 858 ASP cc_start: 0.7744 (t0) cc_final: 0.7265 (m-30) REVERT: G 901 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7991 (tmm) REVERT: N 58 LEU cc_start: 0.8746 (tp) cc_final: 0.8432 (tp) REVERT: N 97 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7890 (pt) REVERT: H 46 TRP cc_start: 0.7737 (m100) cc_final: 0.7436 (m100) REVERT: H 225 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7742 (mp) REVERT: H 262 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7975 (ptpp) REVERT: H 504 LYS cc_start: 0.7611 (tttt) cc_final: 0.7227 (ttpp) REVERT: Q 206 ILE cc_start: 0.9118 (tt) cc_final: 0.8852 (pt) REVERT: J 24 ASP cc_start: 0.7393 (t0) cc_final: 0.6972 (t0) REVERT: L 37 TYR cc_start: 0.8669 (m-80) cc_final: 0.8264 (m-80) REVERT: L 42 TYR cc_start: 0.7705 (t80) cc_final: 0.7319 (t80) REVERT: P 93 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7037 (mp0) outliers start: 93 outliers final: 60 residues processed: 405 average time/residue: 0.2404 time to fit residues: 166.8236 Evaluate side-chains 397 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 326 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain Q residue 181 VAL Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 37 LYS Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 204 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 390 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 342 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.124102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.095168 restraints weight = 88111.770| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.40 r_work: 0.3496 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43659 Z= 0.143 Angle : 0.567 9.437 60455 Z= 0.296 Chirality : 0.040 0.321 6958 Planarity : 0.003 0.042 6640 Dihedral : 21.549 155.019 8621 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 2.20 % Allowed : 15.17 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4626 helix: 0.97 (0.11), residues: 2191 sheet: -0.33 (0.19), residues: 674 loop : -1.35 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 129 TYR 0.015 0.001 TYR D 172 PHE 0.028 0.001 PHE G 853 TRP 0.027 0.001 TRP G 712 HIS 0.003 0.001 HIS G1142 Details of bonding type rmsd covalent geometry : bond 0.00330 (43654) covalent geometry : angle 0.56479 (60449) hydrogen bonds : bond 0.04086 ( 1894) hydrogen bonds : angle 3.76623 ( 5170) metal coordination : bond 0.00597 ( 4) metal coordination : angle 5.42171 ( 6) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 355 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6459 (mp10) REVERT: B 46 MET cc_start: 0.7743 (ptm) cc_final: 0.7488 (ptm) REVERT: B 78 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: B 161 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8131 (pt) REVERT: B 378 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: C 214 ASP cc_start: 0.8340 (m-30) cc_final: 0.8105 (t0) REVERT: C 278 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7856 (tm-30) REVERT: D 144 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: D 326 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8497 (mmm) REVERT: D 443 MET cc_start: 0.7426 (ttt) cc_final: 0.7182 (ttt) REVERT: E 28 GLU cc_start: 0.7944 (tp30) cc_final: 0.7714 (tp30) REVERT: F 213 ARG cc_start: 0.8554 (tpp80) cc_final: 0.8235 (tpp80) REVERT: G 775 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.6264 (m-80) REVERT: G 858 ASP cc_start: 0.7545 (t0) cc_final: 0.7077 (m-30) REVERT: N 58 LEU cc_start: 0.8750 (tp) cc_final: 0.8455 (tp) REVERT: N 97 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7689 (pt) REVERT: H 46 TRP cc_start: 0.7636 (m100) cc_final: 0.7247 (m100) REVERT: H 225 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7732 (mp) REVERT: H 262 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7909 (ptpp) REVERT: H 504 LYS cc_start: 0.7411 (tttt) cc_final: 0.7098 (ttpp) REVERT: Q 206 ILE cc_start: 0.9086 (tt) cc_final: 0.8812 (pt) REVERT: I 80 THR cc_start: 0.8630 (p) cc_final: 0.8422 (p) REVERT: J 24 ASP cc_start: 0.7354 (t0) cc_final: 0.6920 (t0) REVERT: P 93 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6874 (mp0) outliers start: 80 outliers final: 53 residues processed: 412 average time/residue: 0.2412 time to fit residues: 170.2100 Evaluate side-chains 394 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 330 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 415 optimal weight: 0.8980 chunk 360 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 456 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 327 optimal weight: 4.9990 chunk 488 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 439 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN R 327 GLN R 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.124149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095242 restraints weight = 88310.913| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.41 r_work: 0.3496 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43659 Z= 0.143 Angle : 0.564 9.360 60455 Z= 0.294 Chirality : 0.040 0.246 6958 Planarity : 0.003 0.042 6640 Dihedral : 21.483 153.191 8621 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.04 % Rotamer: Outliers : 2.53 % Allowed : 15.56 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4626 helix: 1.05 (0.11), residues: 2199 sheet: -0.31 (0.19), residues: 671 loop : -1.33 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 129 TYR 0.019 0.001 TYR Q 205 PHE 0.027 0.001 PHE G 853 TRP 0.021 0.001 TRP G 712 HIS 0.005 0.001 HIS R 27 Details of bonding type rmsd covalent geometry : bond 0.00330 (43654) covalent geometry : angle 0.56166 (60449) hydrogen bonds : bond 0.04102 ( 1894) hydrogen bonds : angle 3.71701 ( 5170) metal coordination : bond 0.00589 ( 4) metal coordination : angle 5.14980 ( 6) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 356 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: B 46 MET cc_start: 0.7856 (ptm) cc_final: 0.7607 (ptm) REVERT: B 78 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8508 (mt0) REVERT: B 161 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8156 (pt) REVERT: B 378 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: C 214 ASP cc_start: 0.8352 (m-30) cc_final: 0.8093 (t0) REVERT: C 278 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 144 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6989 (pm20) REVERT: D 326 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8513 (mmm) REVERT: E 28 GLU cc_start: 0.7971 (tp30) cc_final: 0.7731 (tp30) REVERT: E 134 GLU cc_start: 0.7426 (tt0) cc_final: 0.7146 (mt-10) REVERT: F 213 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8239 (tpp80) REVERT: G 775 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: G 858 ASP cc_start: 0.7433 (t0) cc_final: 0.7082 (m-30) REVERT: G 901 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7951 (tmm) REVERT: G 962 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8467 (tp) REVERT: N 58 LEU cc_start: 0.8734 (tp) cc_final: 0.8435 (tp) REVERT: N 97 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7704 (pt) REVERT: H 46 TRP cc_start: 0.7586 (m100) cc_final: 0.7174 (m100) REVERT: H 225 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7779 (mp) REVERT: H 262 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7914 (ptpp) REVERT: H 504 LYS cc_start: 0.7406 (tttt) cc_final: 0.7021 (ttpp) REVERT: Q 206 ILE cc_start: 0.9082 (tt) cc_final: 0.8811 (pt) REVERT: J 24 ASP cc_start: 0.7371 (t0) cc_final: 0.6951 (t0) REVERT: P 93 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6909 (mp0) outliers start: 92 outliers final: 63 residues processed: 424 average time/residue: 0.2456 time to fit residues: 177.0519 Evaluate side-chains 411 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 335 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 962 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain Q residue 181 VAL Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 397 optimal weight: 0.7980 chunk 348 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 334 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.115335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084870 restraints weight = 87962.234| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.45 r_work: 0.3302 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 43659 Z= 0.219 Angle : 0.633 8.801 60455 Z= 0.330 Chirality : 0.042 0.269 6958 Planarity : 0.004 0.041 6640 Dihedral : 21.669 150.603 8621 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 3.02 % Allowed : 15.97 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 4626 helix: 0.81 (0.11), residues: 2196 sheet: -0.37 (0.20), residues: 673 loop : -1.43 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 333 TYR 0.017 0.002 TYR D 172 PHE 0.031 0.002 PHE G 853 TRP 0.020 0.002 TRP G 712 HIS 0.005 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00514 (43654) covalent geometry : angle 0.63100 (60449) hydrogen bonds : bond 0.05021 ( 1894) hydrogen bonds : angle 3.98530 ( 5170) metal coordination : bond 0.00716 ( 4) metal coordination : angle 5.63212 ( 6) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 344 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ILE cc_start: 0.5251 (mm) cc_final: 0.4726 (mt) REVERT: A 450 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.6838 (mp10) REVERT: B 78 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: B 161 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8110 (pt) REVERT: B 378 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: C 214 ASP cc_start: 0.8440 (m-30) cc_final: 0.8110 (t0) REVERT: C 278 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7990 (tm-30) REVERT: D 144 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: D 326 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8664 (mtm) REVERT: E 28 GLU cc_start: 0.8129 (tp30) cc_final: 0.7887 (tp30) REVERT: F 213 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8295 (tpp80) REVERT: F 231 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7777 (tm-30) REVERT: G 775 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: G 858 ASP cc_start: 0.7550 (t0) cc_final: 0.7240 (m-30) REVERT: G 901 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8048 (tmm) REVERT: G 932 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: G 962 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8539 (tp) REVERT: N 58 LEU cc_start: 0.8780 (tp) cc_final: 0.8455 (tp) REVERT: N 97 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7988 (pt) REVERT: H 225 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7678 (mp) REVERT: H 262 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7907 (ptpp) REVERT: H 504 LYS cc_start: 0.7606 (tttt) cc_final: 0.7236 (ttpp) REVERT: Q 206 ILE cc_start: 0.9099 (tt) cc_final: 0.8807 (pt) REVERT: I 82 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7751 (mm) REVERT: L 73 ILE cc_start: 0.8439 (mt) cc_final: 0.8071 (mt) REVERT: P 93 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7035 (mp0) outliers start: 110 outliers final: 77 residues processed: 424 average time/residue: 0.2391 time to fit residues: 173.1846 Evaluate side-chains 423 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 331 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 905 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 932 TRP Chi-restraints excluded: chain G residue 962 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain Q residue 181 VAL Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 59 MET Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 284 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 357 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 395 optimal weight: 0.5980 chunk 483 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 442 optimal weight: 0.7980 chunk 473 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 338 ASN H 473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.123806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.094926 restraints weight = 88202.700| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.40 r_work: 0.3489 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43659 Z= 0.140 Angle : 0.576 9.509 60455 Z= 0.300 Chirality : 0.040 0.278 6958 Planarity : 0.003 0.040 6640 Dihedral : 21.536 148.971 8621 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 2.67 % Allowed : 16.79 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.12), residues: 4626 helix: 1.07 (0.11), residues: 2188 sheet: -0.32 (0.20), residues: 674 loop : -1.28 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 129 TYR 0.021 0.001 TYR Q 205 PHE 0.027 0.001 PHE G 853 TRP 0.019 0.001 TRP G 712 HIS 0.004 0.001 HIS R 27 Details of bonding type rmsd covalent geometry : bond 0.00322 (43654) covalent geometry : angle 0.57390 (60449) hydrogen bonds : bond 0.04110 ( 1894) hydrogen bonds : angle 3.73673 ( 5170) metal coordination : bond 0.00561 ( 4) metal coordination : angle 4.99860 ( 6) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 350 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ILE cc_start: 0.5193 (mm) cc_final: 0.4717 (mt) REVERT: A 450 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6442 (mp10) REVERT: B 78 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: B 161 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8186 (pt) REVERT: B 378 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: C 214 ASP cc_start: 0.8349 (m-30) cc_final: 0.8072 (t0) REVERT: D 144 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: D 168 MET cc_start: 0.8173 (mmm) cc_final: 0.7470 (ptm) REVERT: D 326 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8480 (mmm) REVERT: E 28 GLU cc_start: 0.7950 (tp30) cc_final: 0.7727 (tp30) REVERT: F 213 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8301 (tpp80) REVERT: G 775 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: G 858 ASP cc_start: 0.7474 (t0) cc_final: 0.7104 (m-30) REVERT: G 901 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7957 (tmm) REVERT: N 58 LEU cc_start: 0.8717 (tp) cc_final: 0.8390 (tp) REVERT: N 97 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7659 (pt) REVERT: R 327 GLN cc_start: 0.7641 (mp-120) cc_final: 0.7379 (mp10) REVERT: H 46 TRP cc_start: 0.7563 (m100) cc_final: 0.6845 (m100) REVERT: H 225 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7704 (mp) REVERT: H 262 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7903 (ptpp) REVERT: H 504 LYS cc_start: 0.7398 (tttt) cc_final: 0.7012 (ttpp) REVERT: Q 206 ILE cc_start: 0.9154 (tt) cc_final: 0.8882 (pt) REVERT: J 24 ASP cc_start: 0.7313 (t0) cc_final: 0.6867 (t0) REVERT: P 93 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6944 (mp0) outliers start: 97 outliers final: 72 residues processed: 417 average time/residue: 0.2371 time to fit residues: 169.8245 Evaluate side-chains 419 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 335 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 905 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 337 ILE Chi-restraints excluded: chain R residue 338 ASN Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain Q residue 181 VAL Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 59 MET Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 309 optimal weight: 2.9990 chunk 409 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 459 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 237 optimal weight: 0.0980 chunk 438 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.125213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.096522 restraints weight = 87959.342| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.41 r_work: 0.3520 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43659 Z= 0.123 Angle : 0.568 9.851 60455 Z= 0.295 Chirality : 0.040 0.299 6958 Planarity : 0.003 0.041 6640 Dihedral : 21.424 148.025 8621 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 1.95 % Allowed : 17.65 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 4626 helix: 1.22 (0.11), residues: 2184 sheet: -0.21 (0.20), residues: 678 loop : -1.16 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 129 TYR 0.022 0.001 TYR P 40 PHE 0.025 0.001 PHE G 853 TRP 0.030 0.001 TRP G 932 HIS 0.003 0.001 HIS R 27 Details of bonding type rmsd covalent geometry : bond 0.00277 (43654) covalent geometry : angle 0.56595 (60449) hydrogen bonds : bond 0.03856 ( 1894) hydrogen bonds : angle 3.61971 ( 5170) metal coordination : bond 0.00440 ( 4) metal coordination : angle 4.65298 ( 6) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 358 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7089 (mmt) cc_final: 0.6843 (mmt) REVERT: A 450 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6261 (mp10) REVERT: B 78 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8455 (mt0) REVERT: B 161 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8175 (pt) REVERT: B 378 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 214 ASP cc_start: 0.8340 (m-30) cc_final: 0.8057 (t0) REVERT: C 216 GLU cc_start: 0.7733 (tp30) cc_final: 0.6984 (pt0) REVERT: C 260 MET cc_start: 0.7826 (ttp) cc_final: 0.7542 (ttp) REVERT: C 278 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 144 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: D 168 MET cc_start: 0.8110 (mmm) cc_final: 0.7526 (ptm) REVERT: D 326 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8474 (mmm) REVERT: E 28 GLU cc_start: 0.7897 (tp30) cc_final: 0.7676 (tp30) REVERT: E 255 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: F 213 ARG cc_start: 0.8501 (tpp80) cc_final: 0.8266 (tpp80) REVERT: F 231 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7621 (tm-30) REVERT: G 775 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: G 858 ASP cc_start: 0.7495 (t0) cc_final: 0.7167 (m-30) REVERT: G 901 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7963 (tmm) REVERT: G 962 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.7844 (mt) REVERT: N 58 LEU cc_start: 0.8695 (tp) cc_final: 0.8427 (tp) REVERT: N 97 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7578 (pt) REVERT: H 46 TRP cc_start: 0.7574 (m100) cc_final: 0.6886 (m100) REVERT: H 225 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7679 (mp) REVERT: H 262 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7917 (ptpp) REVERT: H 504 LYS cc_start: 0.7366 (tttt) cc_final: 0.6995 (ttpp) REVERT: Q 206 ILE cc_start: 0.9199 (tt) cc_final: 0.8928 (pt) REVERT: J 24 ASP cc_start: 0.7334 (t0) cc_final: 0.6876 (t0) REVERT: P 93 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7019 (mt-10) outliers start: 71 outliers final: 52 residues processed: 409 average time/residue: 0.2300 time to fit residues: 161.4479 Evaluate side-chains 413 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 962 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 59 MET Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 443 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 483 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 446 optimal weight: 0.3980 chunk 260 optimal weight: 3.9990 chunk 282 optimal weight: 8.9990 chunk 290 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.121872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092772 restraints weight = 88787.285| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.38 r_work: 0.3312 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 43659 Z= 0.219 Angle : 0.637 9.903 60455 Z= 0.330 Chirality : 0.042 0.313 6958 Planarity : 0.004 0.041 6640 Dihedral : 21.634 146.785 8621 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 2.03 % Allowed : 17.76 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4626 helix: 0.95 (0.11), residues: 2191 sheet: -0.31 (0.20), residues: 675 loop : -1.29 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 208 TYR 0.019 0.002 TYR Q 178 PHE 0.029 0.001 PHE M 78 TRP 0.038 0.002 TRP G 932 HIS 0.005 0.001 HIS R 27 Details of bonding type rmsd covalent geometry : bond 0.00514 (43654) covalent geometry : angle 0.63453 (60449) hydrogen bonds : bond 0.04869 ( 1894) hydrogen bonds : angle 3.90915 ( 5170) metal coordination : bond 0.00647 ( 4) metal coordination : angle 5.29987 ( 6) Misc. bond : bond 0.00027 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 336 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ILE cc_start: 0.5292 (mm) cc_final: 0.4777 (mt) REVERT: B 78 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: B 161 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8134 (pt) REVERT: B 378 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 214 ASP cc_start: 0.8429 (m-30) cc_final: 0.8125 (t0) REVERT: C 260 MET cc_start: 0.7981 (ttp) cc_final: 0.7723 (ttp) REVERT: C 278 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 144 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: D 168 MET cc_start: 0.8047 (mmm) cc_final: 0.7463 (ptm) REVERT: D 326 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8646 (mtm) REVERT: E 28 GLU cc_start: 0.8079 (tp30) cc_final: 0.7848 (tp30) REVERT: E 255 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: F 213 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8325 (tpp80) REVERT: F 231 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7619 (tm-30) REVERT: G 570 PHE cc_start: 0.7316 (m-80) cc_final: 0.6964 (m-80) REVERT: G 775 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6586 (m-80) REVERT: G 858 ASP cc_start: 0.7578 (t0) cc_final: 0.7273 (m-30) REVERT: G 901 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8119 (tmm) REVERT: G 962 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8502 (tp) REVERT: N 58 LEU cc_start: 0.8764 (tp) cc_final: 0.8456 (tp) REVERT: N 97 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7972 (pt) REVERT: R 327 GLN cc_start: 0.7789 (mp-120) cc_final: 0.7585 (mp10) REVERT: H 225 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7703 (mp) REVERT: H 262 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7805 (ptpp) REVERT: H 504 LYS cc_start: 0.7621 (tttt) cc_final: 0.7261 (ttpp) REVERT: Q 206 ILE cc_start: 0.9235 (tt) cc_final: 0.8986 (pt) REVERT: J 24 ASP cc_start: 0.7407 (t0) cc_final: 0.6945 (t0) REVERT: P 93 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7032 (mp0) outliers start: 74 outliers final: 57 residues processed: 395 average time/residue: 0.2293 time to fit residues: 154.4204 Evaluate side-chains 399 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 775 TYR Chi-restraints excluded: chain G residue 815 VAL Chi-restraints excluded: chain G residue 863 VAL Chi-restraints excluded: chain G residue 901 MET Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 962 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1171 VAL Chi-restraints excluded: chain G residue 1247 MET Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 338 ASN Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 265 CYS Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain Q residue 200 ILE Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain L residue 82 HIS Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 59 MET Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 367 optimal weight: 3.9990 chunk 441 optimal weight: 0.0270 chunk 130 optimal weight: 3.9990 chunk 321 optimal weight: 4.9990 chunk 399 optimal weight: 0.4980 chunk 374 optimal weight: 0.7980 chunk 290 optimal weight: 10.0000 chunk 475 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 398 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.122017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092852 restraints weight = 89218.632| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.39 r_work: 0.3315 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 43659 Z= 0.197 Angle : 0.711 59.200 60455 Z= 0.387 Chirality : 0.041 0.362 6958 Planarity : 0.004 0.041 6640 Dihedral : 21.637 146.814 8621 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 2.31 % Allowed : 17.56 % Favored : 80.13 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4626 helix: 0.96 (0.11), residues: 2190 sheet: -0.32 (0.20), residues: 675 loop : -1.29 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 333 TYR 0.016 0.001 TYR Q 178 PHE 0.030 0.001 PHE G 853 TRP 0.033 0.002 TRP G 932 HIS 0.005 0.001 HIS R 27 Details of bonding type rmsd covalent geometry : bond 0.00453 (43654) covalent geometry : angle 0.70875 (60449) hydrogen bonds : bond 0.04780 ( 1894) hydrogen bonds : angle 3.90815 ( 5170) metal coordination : bond 0.00630 ( 4) metal coordination : angle 5.30851 ( 6) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11240.88 seconds wall clock time: 192 minutes 54.73 seconds (11574.73 seconds total)