Starting phenix.real_space_refine on Fri Mar 6 18:19:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pkx_20369/03_2026/6pkx_20369_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pkx_20369/03_2026/6pkx_20369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pkx_20369/03_2026/6pkx_20369_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pkx_20369/03_2026/6pkx_20369_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pkx_20369/03_2026/6pkx_20369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pkx_20369/03_2026/6pkx_20369.map" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 116 5.16 5 C 20956 2.51 5 N 5670 2.21 5 O 5700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s 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: 32448 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 6710 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 340} Link IDs: {'PTRANS': 32, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 1294 Unresolved non-hydrogen angles: 1615 Unresolved non-hydrogen dihedrals: 1044 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'ASP:plan': 32, 'GLN:plan1': 22, 'GLU:plan': 59, 'ARG:plan': 38, 'HIS:plan': 5, 'ASN:plan1': 14, 'PHE:plan': 11, 'TYR:plan': 6, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 808 Chain: "A" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1339 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 431 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'UNK:plan-1': 22, 'GLN:plan1': 9, 'TYR:plan': 2, 'ASP:plan': 6, 'ARG:plan': 11, 'GLU:plan': 13, 'ASN:plan1': 3, 'HIS:plan': 5, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 255 Chain: "B" Number of atoms: 6761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 6761 Classifications: {'peptide': 997} Incomplete info: {'truncation_to_alanine': 373} Link IDs: {'PTRANS': 32, 'TRANS': 964} Chain breaks: 9 Unresolved non-hydrogen bonds: 1357 Unresolved non-hydrogen angles: 1682 Unresolved non-hydrogen dihedrals: 1087 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLU:plan': 61, 'ASN:plan1': 17, 'ARG:plan': 38, 'ASP:plan': 34, 'PHE:plan': 9, 'GLN:plan1': 25, 'TYR:plan': 6, 'HIS:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 812 Chain: "B" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1377 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 14, 'TRANS': 206} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'UNK:plan-1': 22, 'HIS:plan': 5, 'ASP:plan': 7, 'ARG:plan': 11, 'GLU:plan': 13, 'ASN:plan1': 3, 'GLN:plan1': 8, 'PHE:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 238 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'AR6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLU A1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A1272 " occ=0.50 residue: pdb=" N VAL A1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A1400 " occ=0.50 residue: pdb=" N ARG A1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG A1447 " occ=0.50 residue: pdb=" N GLU B1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B1272 " occ=0.50 residue: pdb=" N VAL B1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B1400 " occ=0.50 residue: pdb=" N ARG B1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG B1447 " occ=0.50 residue: pdb=" N GLU C1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU C1272 " occ=0.50 residue: pdb=" N VAL C1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C1400 " occ=0.50 residue: pdb=" N ARG C1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG C1447 " occ=0.50 residue: pdb=" N GLU D1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D1272 " occ=0.50 residue: pdb=" N VAL D1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D1400 " occ=0.50 residue: pdb=" N ARG D1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG D1447 " occ=0.50 Time building chain proxies: 15.02, per 1000 atoms: 0.46 Number of scatterers: 32448 At special positions: 0 Unit cell: (165.41, 162.63, 179.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 116 16.00 P 4 15.00 O 5700 8.00 N 5670 7.00 C 20956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.02 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1024 " distance=2.01 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.00 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1024 " distance=2.06 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.02 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1024 " distance=2.01 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.00 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1024 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9208 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 14 sheets defined 61.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.852A pdb=" N HIS A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.516A pdb=" N LEU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.521A pdb=" N ARG A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.988A pdb=" N ILE A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.243A pdb=" N LYS A 368 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 370 " --> pdb=" O TYR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.865A pdb=" N MET A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 426 through 439 Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.582A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.541A pdb=" N GLY A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.581A pdb=" N LEU A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.997A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.556A pdb=" N ARG A 510 " --> pdb=" O CYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 548 Processing helix chain 'A' and resid 593 through 605 removed outlier: 3.538A pdb=" N ASP A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 605 " --> pdb=" O TRP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 620 through 640 removed outlier: 3.709A pdb=" N ALA A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 672 removed outlier: 3.598A pdb=" N ASP A 672 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.617A pdb=" N ARG A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.513A pdb=" N PHE A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.002A pdb=" N ILE A 741 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 742 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 743 " --> pdb=" O LEU A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 743' Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 808 through 834 Processing helix chain 'A' and resid 840 through 864 removed outlier: 3.695A pdb=" N THR A 851 " --> pdb=" O TYR A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 877 Processing helix chain 'A' and resid 882 through 901 removed outlier: 4.249A pdb=" N ILE A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 923 Processing helix chain 'A' and resid 924 through 930 removed outlier: 4.541A pdb=" N ALA A 928 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 930 " --> pdb=" O MET A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 973 removed outlier: 4.756A pdb=" N LEU A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 992 removed outlier: 4.735A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 990 - end of helix Processing helix chain 'A' and resid 993 through 995 No H-bonds generated for 'chain 'A' and resid 993 through 995' Processing helix chain 'A' and resid 1000 through 1004 removed outlier: 3.646A pdb=" N ASP A1003 " --> pdb=" O THR A1000 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A1004 " --> pdb=" O ASN A1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1000 through 1004' Processing helix chain 'A' and resid 1038 through 1067 removed outlier: 3.913A pdb=" N MET A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A1049 " --> pdb=" O CYS A1045 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A1050 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A1066 " --> pdb=" O ILE A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1071 Processing helix chain 'A' and resid 1073 through 1092 removed outlier: 3.772A pdb=" N ILE A1077 " --> pdb=" O ASN A1073 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1085 " --> pdb=" O GLN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1129 through 1157 Processing helix chain 'A' and resid 1158 through 1184 Processing helix chain 'A' and resid 1189 through 1209 Processing helix chain 'A' and resid 1252 through 1256 removed outlier: 3.660A pdb=" N ARG A1255 " --> pdb=" O MET A1252 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A1256 " --> pdb=" O PHE A1253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1252 through 1256' Processing helix chain 'A' and resid 1370 through 1380 Processing helix chain 'A' and resid 1427 through 1432 Processing helix chain 'A' and resid 1437 through 1441 Processing helix chain 'A' and resid 1456 through 1469 removed outlier: 3.611A pdb=" N ALA A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 178 removed outlier: 4.101A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.789A pdb=" N ARG B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 removed outlier: 4.014A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.563A pdb=" N PHE B 370 " --> pdb=" O TYR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.608A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 4.441A pdb=" N ARG B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.737A pdb=" N ALA B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.758A pdb=" N PHE B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.713A pdb=" N LEU B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 502 removed outlier: 4.076A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.791A pdb=" N ARG B 510 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 3.969A pdb=" N SER B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU B 542 " --> pdb=" O HIS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 606 removed outlier: 3.527A pdb=" N ASP B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 removed outlier: 4.029A pdb=" N ILE B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 617 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 638 Processing helix chain 'B' and resid 643 through 672 Processing helix chain 'B' and resid 673 through 681 removed outlier: 3.941A pdb=" N ILE B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 707 through 720 removed outlier: 3.644A pdb=" N GLY B 720 " --> pdb=" O GLN B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 737 removed outlier: 3.714A pdb=" N VAL B 731 " --> pdb=" O PRO B 727 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.624A pdb=" N THR B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.585A pdb=" N THR B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 808 through 833 removed outlier: 3.598A pdb=" N LYS B 812 " --> pdb=" O SER B 808 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 864 Processing helix chain 'B' and resid 870 through 879 removed outlier: 3.500A pdb=" N LYS B 879 " --> pdb=" O LYS B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 899 removed outlier: 3.809A pdb=" N LEU B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 928 Processing helix chain 'B' and resid 936 through 972 removed outlier: 3.598A pdb=" N ASP B 949 " --> pdb=" O ARG B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 987 removed outlier: 3.790A pdb=" N ILE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 996 removed outlier: 3.802A pdb=" N THR B 993 " --> pdb=" O GLU B 989 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 996 " --> pdb=" O ILE B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1071 removed outlier: 4.073A pdb=" N THR B1040 " --> pdb=" O PRO B1036 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1090 removed outlier: 3.589A pdb=" N PHE B1080 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS B1090 " --> pdb=" O ILE B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1109 removed outlier: 5.267A pdb=" N LEU B1102 " --> pdb=" O PRO B1098 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B1105 " --> pdb=" O LEU B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1156 removed outlier: 3.508A pdb=" N GLU B1133 " --> pdb=" O GLU B1129 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU B1134 " --> pdb=" O GLN B1130 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU B1135 " --> pdb=" O THR B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1183 removed outlier: 4.576A pdb=" N HIS B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1209 Processing helix chain 'B' and resid 1251 through 1256 removed outlier: 3.548A pdb=" N GLN B1256 " --> pdb=" O PHE B1253 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1427 through 1433 removed outlier: 4.224A pdb=" N MET B1433 " --> pdb=" O ASP B1429 " (cutoff:3.500A) Processing helix chain 'B' and resid 1451 through 1455 removed outlier: 4.032A pdb=" N CYS B1454 " --> pdb=" O SER B1451 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG B1455 " --> pdb=" O ASP B1452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1451 through 1455' Processing helix chain 'B' and resid 1456 through 1470 removed outlier: 3.593A pdb=" N HIS B1470 " --> pdb=" O ILE B1466 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 159 through 176 Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.851A pdb=" N HIS C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 204 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.515A pdb=" N LEU C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.520A pdb=" N ARG C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.987A pdb=" N ILE C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.244A pdb=" N LYS C 368 " --> pdb=" O GLN C 365 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 370 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 388 removed outlier: 3.865A pdb=" N MET C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 418 Processing helix chain 'C' and resid 426 through 439 Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.583A pdb=" N ALA C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 470 removed outlier: 3.541A pdb=" N GLY C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.580A pdb=" N LEU C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.997A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 517 removed outlier: 3.555A pdb=" N ARG C 510 " --> pdb=" O CYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 548 Processing helix chain 'C' and resid 593 through 605 removed outlier: 3.539A pdb=" N ASP C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP C 601 " --> pdb=" O ASP C 597 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 605 " --> pdb=" O TRP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 620 through 640 removed outlier: 3.709A pdb=" N ALA C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 640 " --> pdb=" O ALA C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 672 removed outlier: 3.598A pdb=" N ASP C 672 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 682 removed outlier: 3.617A pdb=" N ARG C 682 " --> pdb=" O LYS C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 700 Processing helix chain 'C' and resid 707 through 719 Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.513A pdb=" N PHE C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 removed outlier: 4.001A pdb=" N ILE C 741 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C 742 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 743 " --> pdb=" O LEU C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 743' Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 808 through 834 Processing helix chain 'C' and resid 840 through 864 removed outlier: 3.696A pdb=" N THR C 851 " --> pdb=" O TYR C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 877 Processing helix chain 'C' and resid 882 through 901 removed outlier: 4.250A pdb=" N ILE C 894 " --> pdb=" O ILE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 923 Processing helix chain 'C' and resid 924 through 930 removed outlier: 4.542A pdb=" N ALA C 928 " --> pdb=" O ARG C 925 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 930 " --> pdb=" O MET C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 973 removed outlier: 4.756A pdb=" N LEU C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE C 973 " --> pdb=" O GLN C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 992 removed outlier: 4.735A pdb=" N GLU C 989 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Proline residue: C 990 - end of helix Processing helix chain 'C' and resid 993 through 995 No H-bonds generated for 'chain 'C' and resid 993 through 995' Processing helix chain 'C' and resid 1000 through 1004 removed outlier: 3.646A pdb=" N ASP C1003 " --> pdb=" O THR C1000 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C1004 " --> pdb=" O ASN C1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1000 through 1004' Processing helix chain 'C' and resid 1038 through 1067 removed outlier: 3.913A pdb=" N MET C1043 " --> pdb=" O LEU C1039 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS C1045 " --> pdb=" O ILE C1041 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C1049 " --> pdb=" O CYS C1045 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE C1050 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C1066 " --> pdb=" O ILE C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1071 Processing helix chain 'C' and resid 1073 through 1092 removed outlier: 3.772A pdb=" N ILE C1077 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU C1084 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C1085 " --> pdb=" O GLN C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1112 Processing helix chain 'C' and resid 1129 through 1157 Processing helix chain 'C' and resid 1158 through 1184 Processing helix chain 'C' and resid 1189 through 1209 Processing helix chain 'C' and resid 1252 through 1256 removed outlier: 3.660A pdb=" N ARG C1255 " --> pdb=" O MET C1252 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN C1256 " --> pdb=" O PHE C1253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1252 through 1256' Processing helix chain 'C' and resid 1370 through 1380 Processing helix chain 'C' and resid 1427 through 1432 Processing helix chain 'C' and resid 1437 through 1441 Processing helix chain 'C' and resid 1456 through 1469 removed outlier: 3.610A pdb=" N ALA C1467 " --> pdb=" O LEU C1463 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 178 removed outlier: 4.102A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 274 through 288 removed outlier: 3.789A pdb=" N ARG D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 321 removed outlier: 4.014A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.563A pdb=" N PHE D 370 " --> pdb=" O TYR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 404 through 419 removed outlier: 3.608A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 removed outlier: 4.441A pdb=" N ARG D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 440 through 448 removed outlier: 3.737A pdb=" N ALA D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.758A pdb=" N PHE D 465 " --> pdb=" O HIS D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.713A pdb=" N LEU D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 502 removed outlier: 4.076A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 517 removed outlier: 3.790A pdb=" N ARG D 510 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG D 515 " --> pdb=" O LYS D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 547 removed outlier: 3.969A pdb=" N SER D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU D 542 " --> pdb=" O HIS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 606 removed outlier: 3.527A pdb=" N ASP D 597 " --> pdb=" O ASP D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 617 removed outlier: 4.029A pdb=" N ILE D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN D 617 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 638 Processing helix chain 'D' and resid 643 through 672 Processing helix chain 'D' and resid 673 through 681 removed outlier: 3.941A pdb=" N ILE D 681 " --> pdb=" O GLN D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 700 Processing helix chain 'D' and resid 707 through 720 removed outlier: 3.644A pdb=" N GLY D 720 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 737 removed outlier: 3.715A pdb=" N VAL D 731 " --> pdb=" O PRO D 727 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 removed outlier: 3.624A pdb=" N THR D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.586A pdb=" N THR D 761 " --> pdb=" O GLN D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 807 Processing helix chain 'D' and resid 808 through 833 removed outlier: 3.597A pdb=" N LYS D 812 " --> pdb=" O SER D 808 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 864 Processing helix chain 'D' and resid 870 through 879 Processing helix chain 'D' and resid 881 through 899 removed outlier: 3.810A pdb=" N LEU D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 928 Processing helix chain 'D' and resid 936 through 972 removed outlier: 3.599A pdb=" N ASP D 949 " --> pdb=" O ARG D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 987 removed outlier: 3.790A pdb=" N ILE D 983 " --> pdb=" O LEU D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 996 removed outlier: 3.802A pdb=" N THR D 993 " --> pdb=" O GLU D 989 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY D 996 " --> pdb=" O ILE D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1071 removed outlier: 4.073A pdb=" N THR D1040 " --> pdb=" O PRO D1036 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1090 removed outlier: 3.589A pdb=" N PHE D1080 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS D1090 " --> pdb=" O ILE D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1109 removed outlier: 5.269A pdb=" N LEU D1102 " --> pdb=" O PRO D1098 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D1105 " --> pdb=" O LEU D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1156 removed outlier: 3.509A pdb=" N GLU D1133 " --> pdb=" O GLU D1129 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU D1134 " --> pdb=" O GLN D1130 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU D1135 " --> pdb=" O THR D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1183 removed outlier: 4.576A pdb=" N HIS D1164 " --> pdb=" O GLU D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1189 through 1209 Processing helix chain 'D' and resid 1251 through 1256 removed outlier: 3.549A pdb=" N GLN D1256 " --> pdb=" O PHE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1370 through 1381 Processing helix chain 'D' and resid 1427 through 1433 removed outlier: 4.225A pdb=" N MET D1433 " --> pdb=" O ASP D1429 " (cutoff:3.500A) Processing helix chain 'D' and resid 1451 through 1455 removed outlier: 4.032A pdb=" N CYS D1454 " --> pdb=" O SER D1451 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG D1455 " --> pdb=" O ASP D1452 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1451 through 1455' Processing helix chain 'D' and resid 1456 through 1470 removed outlier: 3.594A pdb=" N HIS D1470 " --> pdb=" O ILE D1466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 239 removed outlier: 7.798A pdb=" N ALA A 238 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP A 105 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 214 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU A 261 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 216 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A 263 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 218 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 147 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N GLY A 184 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL A 149 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 302 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL A 327 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 305 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE A 395 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 328 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 3.835A pdb=" N GLY A1361 " --> pdb=" O LEU A1328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1333 through 1334 removed outlier: 3.664A pdb=" N ARG A1334 " --> pdb=" O GLU A1344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'B' and resid 237 through 238 removed outlier: 6.940A pdb=" N ASP B 105 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS B 117 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU B 262 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 119 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP B 264 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 121 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 214 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU B 261 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY B 216 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 263 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 218 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE B 181 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL B 217 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY B 184 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 146 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 304 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 148 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL B 327 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 305 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1325 through 1329 removed outlier: 5.810A pdb=" N ASN B1325 " --> pdb=" O GLU B1412 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N SER B1414 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B1327 " --> pdb=" O SER B1414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1345 through 1348 Processing sheet with id=AA8, first strand: chain 'C' and resid 237 through 239 removed outlier: 7.798A pdb=" N ALA C 238 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP C 105 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 214 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU C 261 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 216 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL C 263 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 218 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N GLY C 184 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL C 149 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 302 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 327 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 305 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N CYS C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE C 395 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL C 328 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 3.834A pdb=" N GLY C1361 " --> pdb=" O LEU C1328 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1333 through 1334 removed outlier: 3.664A pdb=" N ARG C1334 " --> pdb=" O GLU C1344 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AB3, first strand: chain 'D' and resid 237 through 238 removed outlier: 6.939A pdb=" N ASP D 105 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS D 117 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU D 262 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 119 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP D 264 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL D 121 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 214 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU D 261 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY D 216 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL D 263 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA D 218 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE D 181 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL D 217 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY D 184 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 146 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL D 304 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER D 148 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL D 327 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 305 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1325 through 1329 removed outlier: 5.811A pdb=" N ASN D1325 " --> pdb=" O GLU D1412 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N SER D1414 " --> pdb=" O ASN D1325 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE D1327 " --> pdb=" O SER D1414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1345 through 1348 1975 hydrogen bonds defined for protein. 5817 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10581 1.34 - 1.46: 8386 1.46 - 1.59: 14047 1.59 - 1.71: 12 1.71 - 1.83: 164 Bond restraints: 33190 Sorted by residual: bond pdb=" C3D AR6 D1602 " pdb=" C4D AR6 D1602 " ideal model delta sigma weight residual 1.529 1.300 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3D AR6 B1602 " pdb=" C4D AR6 B1602 " ideal model delta sigma weight residual 1.529 1.300 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1' AR6 B1602 " pdb=" C2' AR6 B1602 " ideal model delta sigma weight residual 1.529 1.304 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' AR6 D1602 " pdb=" C2' AR6 D1602 " ideal model delta sigma weight residual 1.529 1.304 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C1' AR6 B1602 " pdb=" O4' AR6 B1602 " ideal model delta sigma weight residual 1.396 1.608 -0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 33185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 44863 3.18 - 6.36: 713 6.36 - 9.54: 122 9.54 - 12.72: 12 12.72 - 15.90: 4 Bond angle restraints: 45714 Sorted by residual: angle pdb=" N ILE D 275 " pdb=" CA ILE D 275 " pdb=" C ILE D 275 " ideal model delta sigma weight residual 110.62 118.74 -8.12 1.02e+00 9.61e-01 6.35e+01 angle pdb=" N ILE B 275 " pdb=" CA ILE B 275 " pdb=" C ILE B 275 " ideal model delta sigma weight residual 110.62 118.73 -8.11 1.02e+00 9.61e-01 6.32e+01 angle pdb=" N GLY D 272 " pdb=" CA GLY D 272 " pdb=" C GLY D 272 " ideal model delta sigma weight residual 113.24 123.63 -10.39 1.31e+00 5.83e-01 6.29e+01 angle pdb=" N GLY B 272 " pdb=" CA GLY B 272 " pdb=" C GLY B 272 " ideal model delta sigma weight residual 113.24 123.61 -10.37 1.31e+00 5.83e-01 6.27e+01 angle pdb=" N ARG D 278 " pdb=" CA ARG D 278 " pdb=" C ARG D 278 " ideal model delta sigma weight residual 111.07 119.18 -8.11 1.07e+00 8.73e-01 5.74e+01 ... (remaining 45709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 17890 15.16 - 30.31: 902 30.31 - 45.47: 200 45.47 - 60.62: 42 60.62 - 75.78: 22 Dihedral angle restraints: 19056 sinusoidal: 4954 harmonic: 14102 Sorted by residual: dihedral pdb=" CA SER D1011 " pdb=" C SER D1011 " pdb=" N CYS D1012 " pdb=" CA CYS D1012 " ideal model delta harmonic sigma weight residual 180.00 125.40 54.60 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA SER B1011 " pdb=" C SER B1011 " pdb=" N CYS B1012 " pdb=" CA CYS B1012 " ideal model delta harmonic sigma weight residual 180.00 125.47 54.53 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ASP A 620 " pdb=" C ASP A 620 " pdb=" N CYS A 621 " pdb=" CA CYS A 621 " ideal model delta harmonic sigma weight residual -180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 19053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4687 0.072 - 0.144: 796 0.144 - 0.216: 82 0.216 - 0.288: 15 0.288 - 0.360: 4 Chirality restraints: 5584 Sorted by residual: chirality pdb=" CA CYS B1012 " pdb=" N CYS B1012 " pdb=" C CYS B1012 " pdb=" CB CYS B1012 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA CYS D1012 " pdb=" N CYS D1012 " pdb=" C CYS D1012 " pdb=" CB CYS D1012 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ARG D 278 " pdb=" N ARG D 278 " pdb=" C ARG D 278 " pdb=" CB ARG D 278 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 5581 not shown) Planarity restraints: 5844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 592 " 0.018 2.00e-02 2.50e+03 1.95e-02 9.47e+00 pdb=" CG TRP B 592 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 592 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 592 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 592 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 592 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 592 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 592 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP B 592 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 592 " -0.019 2.00e-02 2.50e+03 1.94e-02 9.45e+00 pdb=" CG TRP D 592 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 592 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 592 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 592 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 592 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 592 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 592 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 592 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP D 592 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 378 " 0.017 2.00e-02 2.50e+03 1.91e-02 9.10e+00 pdb=" CG TRP B 378 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 378 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 378 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 378 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 378 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 378 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 378 " -0.010 2.00e-02 2.50e+03 ... (remaining 5841 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 832 2.70 - 3.25: 32059 3.25 - 3.80: 50635 3.80 - 4.35: 55562 4.35 - 4.90: 91971 Nonbonded interactions: 231059 Sorted by model distance: nonbonded pdb=" O ARG D 249 " pdb=" OH TYR D 271 " model vdw 2.151 3.040 nonbonded pdb=" O ARG B 249 " pdb=" OH TYR B 271 " model vdw 2.151 3.040 nonbonded pdb=" CB UNK B1209 " pdb=" CB UNK C1209 " model vdw 2.190 3.840 nonbonded pdb=" CB UNK A1209 " pdb=" CB UNK D1209 " model vdw 2.229 3.840 nonbonded pdb=" OD1 ASN D 356 " pdb=" OH TYR D 367 " model vdw 2.316 3.040 ... (remaining 231054 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.160 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.008 0.229 33198 Z= 0.361 Angle : 1.024 15.898 45730 Z= 0.560 Chirality : 0.055 0.360 5584 Planarity : 0.007 0.070 5844 Dihedral : 11.028 75.776 9824 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.10), residues: 4640 helix: -2.18 (0.08), residues: 2542 sheet: -1.98 (0.30), residues: 278 loop : -3.33 (0.12), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1082 TYR 0.036 0.003 TYR C 847 PHE 0.026 0.003 PHE B 156 TRP 0.052 0.004 TRP B 378 HIS 0.009 0.002 HIS B1329 Details of bonding type rmsd covalent geometry : bond 0.00760 (33190) covalent geometry : angle 1.02370 (45714) SS BOND : bond 0.02483 ( 8) SS BOND : angle 1.97147 ( 16) hydrogen bonds : bond 0.14229 ( 1975) hydrogen bonds : angle 6.46233 ( 5817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1154 ASP cc_start: 0.8221 (m-30) cc_final: 0.8001 (m-30) REVERT: A 1173 MET cc_start: 0.6975 (ttp) cc_final: 0.6692 (ttm) REVERT: B 410 LEU cc_start: 0.9276 (mt) cc_final: 0.9029 (tp) REVERT: B 601 TRP cc_start: 0.8790 (t60) cc_final: 0.8518 (t60) REVERT: B 669 HIS cc_start: 0.8312 (t70) cc_final: 0.8003 (t-90) REVERT: B 923 CYS cc_start: 0.8078 (t) cc_final: 0.7602 (t) REVERT: B 1045 CYS cc_start: 0.8312 (m) cc_final: 0.7998 (t) REVERT: B 1252 MET cc_start: 0.7176 (mtm) cc_final: 0.6650 (pmm) REVERT: B 1290 GLN cc_start: 0.6786 (mm-40) cc_final: 0.6256 (pt0) REVERT: B 1305 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7376 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3395 (m100) cc_final: 0.2442 (m100) REVERT: B 1356 TRP cc_start: 0.5727 (m-90) cc_final: 0.5367 (m100) REVERT: C 1154 ASP cc_start: 0.8236 (m-30) cc_final: 0.7984 (m-30) REVERT: C 1173 MET cc_start: 0.6978 (ttp) cc_final: 0.6683 (ttm) REVERT: D 410 LEU cc_start: 0.9281 (mt) cc_final: 0.9029 (tp) REVERT: D 601 TRP cc_start: 0.8798 (t60) cc_final: 0.8590 (t60) REVERT: D 669 HIS cc_start: 0.8319 (t70) cc_final: 0.8037 (t70) REVERT: D 923 CYS cc_start: 0.7929 (t) cc_final: 0.7471 (t) REVERT: D 1045 CYS cc_start: 0.8225 (m) cc_final: 0.7964 (t) REVERT: D 1252 MET cc_start: 0.7176 (mtm) cc_final: 0.6649 (pmm) REVERT: D 1290 GLN cc_start: 0.6792 (mm-40) cc_final: 0.6257 (pt0) REVERT: D 1305 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7476 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3410 (m100) cc_final: 0.2473 (m100) REVERT: D 1356 TRP cc_start: 0.5734 (m-90) cc_final: 0.5369 (m100) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 0.1670 time to fit residues: 177.3934 Evaluate side-chains 356 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.0000 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 256 ASN A 259 HIS A 341 HIS A1064 ASN A1081 GLN B 193 HIS B 259 HIS B 707 HIS B1164 HIS C 187 HIS C 256 ASN C 259 HIS C 341 HIS C1064 ASN C1081 GLN D 193 HIS D 259 HIS D 707 HIS D1164 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.162097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128143 restraints weight = 82399.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126653 restraints weight = 92566.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127566 restraints weight = 78883.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126864 restraints weight = 58312.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127096 restraints weight = 55134.557| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33198 Z= 0.153 Angle : 0.630 7.951 45730 Z= 0.334 Chirality : 0.040 0.281 5584 Planarity : 0.005 0.062 5844 Dihedral : 6.107 83.674 5086 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.59 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4640 helix: -0.10 (0.10), residues: 2568 sheet: -1.96 (0.29), residues: 276 loop : -2.88 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1162 TYR 0.019 0.002 TYR D1083 PHE 0.024 0.002 PHE C 922 TRP 0.024 0.002 TRP D 592 HIS 0.005 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00326 (33190) covalent geometry : angle 0.62911 (45714) SS BOND : bond 0.00772 ( 8) SS BOND : angle 1.72888 ( 16) hydrogen bonds : bond 0.04441 ( 1975) hydrogen bonds : angle 4.39990 ( 5817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 832 MET cc_start: 0.6003 (ttp) cc_final: 0.5733 (ttp) REVERT: A 1049 LEU cc_start: 0.7425 (pp) cc_final: 0.7128 (tp) REVERT: A 1173 MET cc_start: 0.8025 (ttp) cc_final: 0.7759 (ttm) REVERT: B 171 ILE cc_start: 0.9085 (mm) cc_final: 0.8518 (tt) REVERT: B 410 LEU cc_start: 0.9062 (mt) cc_final: 0.8804 (tp) REVERT: B 669 HIS cc_start: 0.8263 (t70) cc_final: 0.7933 (t-90) REVERT: B 1045 CYS cc_start: 0.8354 (m) cc_final: 0.8073 (p) REVERT: B 1252 MET cc_start: 0.7533 (mtm) cc_final: 0.7156 (pmm) REVERT: B 1305 ARG cc_start: 0.7601 (mtm180) cc_final: 0.7373 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3507 (m100) cc_final: 0.2569 (m100) REVERT: B 1356 TRP cc_start: 0.6127 (m-90) cc_final: 0.5820 (m100) REVERT: C 832 MET cc_start: 0.6290 (ttp) cc_final: 0.5985 (ttp) REVERT: C 1049 LEU cc_start: 0.7408 (pp) cc_final: 0.7161 (tp) REVERT: C 1173 MET cc_start: 0.8023 (ttp) cc_final: 0.7746 (ttm) REVERT: D 171 ILE cc_start: 0.9095 (mm) cc_final: 0.8481 (tt) REVERT: D 410 LEU cc_start: 0.9083 (mt) cc_final: 0.8813 (tp) REVERT: D 468 LEU cc_start: 0.9378 (tt) cc_final: 0.9150 (tp) REVERT: D 669 HIS cc_start: 0.8283 (t70) cc_final: 0.7937 (t-90) REVERT: D 1045 CYS cc_start: 0.8388 (m) cc_final: 0.8056 (p) REVERT: D 1085 LEU cc_start: 0.8966 (tp) cc_final: 0.8764 (mt) REVERT: D 1252 MET cc_start: 0.7246 (mtm) cc_final: 0.7041 (pmm) REVERT: D 1305 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7361 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3447 (m100) cc_final: 0.2599 (m100) REVERT: D 1356 TRP cc_start: 0.5889 (m-90) cc_final: 0.5688 (m100) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1503 time to fit residues: 122.6043 Evaluate side-chains 352 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 384 optimal weight: 0.0010 chunk 22 optimal weight: 40.0000 chunk 242 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 375 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 379 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 HIS A1161 HIS B 259 HIS B 390 HIS C 707 HIS C1161 HIS D 259 HIS D 390 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.158260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124926 restraints weight = 82442.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122946 restraints weight = 108860.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123623 restraints weight = 101577.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123757 restraints weight = 71426.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.124118 restraints weight = 58202.767| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33198 Z= 0.208 Angle : 0.668 9.165 45730 Z= 0.353 Chirality : 0.042 0.301 5584 Planarity : 0.005 0.054 5844 Dihedral : 5.778 83.102 5086 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 4640 helix: 0.46 (0.10), residues: 2600 sheet: -2.00 (0.27), residues: 302 loop : -2.73 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1305 TYR 0.025 0.002 TYR D1083 PHE 0.026 0.002 PHE A 922 TRP 0.055 0.002 TRP B 815 HIS 0.009 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00462 (33190) covalent geometry : angle 0.66723 (45714) SS BOND : bond 0.00817 ( 8) SS BOND : angle 2.22067 ( 16) hydrogen bonds : bond 0.04705 ( 1975) hydrogen bonds : angle 4.38378 ( 5817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 MET cc_start: 0.7931 (ttp) cc_final: 0.7681 (ttm) REVERT: B 171 ILE cc_start: 0.9156 (mm) cc_final: 0.8576 (tt) REVERT: B 1045 CYS cc_start: 0.8295 (m) cc_final: 0.8095 (p) REVERT: B 1252 MET cc_start: 0.7557 (mtm) cc_final: 0.7262 (pmm) REVERT: B 1305 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7450 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3583 (m100) cc_final: 0.2688 (m100) REVERT: C 1173 MET cc_start: 0.7867 (ttp) cc_final: 0.7611 (ttm) REVERT: D 171 ILE cc_start: 0.9112 (mm) cc_final: 0.8507 (tt) REVERT: D 1045 CYS cc_start: 0.8316 (m) cc_final: 0.8075 (p) REVERT: D 1252 MET cc_start: 0.7532 (mtm) cc_final: 0.7223 (pmm) REVERT: D 1305 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7370 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3589 (m100) cc_final: 0.2706 (m100) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1499 time to fit residues: 103.2377 Evaluate side-chains 306 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 362 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 299 optimal weight: 30.0000 chunk 64 optimal weight: 0.0570 chunk 268 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 459 optimal weight: 50.0000 chunk 119 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 335 optimal weight: 2.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN B 426 HIS B 660 GLN C 726 ASN D 426 HIS D 660 GLN D 816 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.157416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124163 restraints weight = 82794.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.121619 restraints weight = 110814.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122633 restraints weight = 101763.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122556 restraints weight = 71143.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122889 restraints weight = 60791.824| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33198 Z= 0.199 Angle : 0.642 8.748 45730 Z= 0.339 Chirality : 0.042 0.300 5584 Planarity : 0.005 0.047 5844 Dihedral : 5.637 82.275 5086 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.50 % Rotamer: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 4640 helix: 0.75 (0.10), residues: 2598 sheet: -1.88 (0.29), residues: 292 loop : -2.58 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 477 TYR 0.025 0.002 TYR D1083 PHE 0.025 0.002 PHE C 922 TRP 0.063 0.002 TRP B 592 HIS 0.006 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00441 (33190) covalent geometry : angle 0.64059 (45714) SS BOND : bond 0.00322 ( 8) SS BOND : angle 2.45652 ( 16) hydrogen bonds : bond 0.04486 ( 1975) hydrogen bonds : angle 4.27158 ( 5817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 388 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 MET cc_start: 0.8382 (mtm) cc_final: 0.8137 (mtm) REVERT: A 1173 MET cc_start: 0.7910 (ttp) cc_final: 0.7651 (ttm) REVERT: B 1124 PHE cc_start: 0.8190 (m-80) cc_final: 0.7953 (m-10) REVERT: B 1143 MET cc_start: 0.8449 (mmm) cc_final: 0.7802 (mmt) REVERT: B 1335 TRP cc_start: 0.3673 (m100) cc_final: 0.2745 (m100) REVERT: C 650 MET cc_start: 0.8383 (mtm) cc_final: 0.8149 (mtm) REVERT: C 1049 LEU cc_start: 0.7417 (pp) cc_final: 0.7000 (tp) REVERT: C 1173 MET cc_start: 0.7894 (ttp) cc_final: 0.7627 (ttm) REVERT: D 1045 CYS cc_start: 0.8292 (m) cc_final: 0.8062 (p) REVERT: D 1143 MET cc_start: 0.8444 (mmm) cc_final: 0.7815 (mmt) REVERT: D 1305 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7375 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3690 (m100) cc_final: 0.2769 (m100) outliers start: 2 outliers final: 0 residues processed: 390 average time/residue: 0.1412 time to fit residues: 99.6401 Evaluate side-chains 300 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 158 optimal weight: 3.9990 chunk 381 optimal weight: 0.9990 chunk 467 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 353 optimal weight: 30.0000 chunk 103 optimal weight: 0.0670 chunk 409 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 397 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN B 426 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN D 426 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.159699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123568 restraints weight = 82665.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118412 restraints weight = 97686.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.119424 restraints weight = 81397.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119960 restraints weight = 57419.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120057 restraints weight = 50102.563| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33198 Z= 0.139 Angle : 0.578 6.651 45730 Z= 0.302 Chirality : 0.039 0.245 5584 Planarity : 0.004 0.044 5844 Dihedral : 5.351 82.328 5086 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 0.08 % Allowed : 2.76 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4640 helix: 1.09 (0.10), residues: 2614 sheet: -2.08 (0.28), residues: 316 loop : -2.46 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1255 TYR 0.019 0.001 TYR D1083 PHE 0.023 0.001 PHE A 922 TRP 0.038 0.002 TRP A 592 HIS 0.004 0.001 HIS B1329 Details of bonding type rmsd covalent geometry : bond 0.00305 (33190) covalent geometry : angle 0.57656 (45714) SS BOND : bond 0.00573 ( 8) SS BOND : angle 2.00240 ( 16) hydrogen bonds : bond 0.03962 ( 1975) hydrogen bonds : angle 3.95721 ( 5817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.3292 (mmt) cc_final: 0.2115 (tpt) REVERT: A 1173 MET cc_start: 0.8011 (ttp) cc_final: 0.7721 (ttm) REVERT: B 171 ILE cc_start: 0.9040 (mm) cc_final: 0.8536 (tt) REVERT: B 1026 MET cc_start: 0.7796 (tpp) cc_final: 0.7595 (tpp) REVERT: B 1124 PHE cc_start: 0.8232 (m-80) cc_final: 0.8010 (m-10) REVERT: B 1335 TRP cc_start: 0.3690 (m100) cc_final: 0.2668 (m100) REVERT: C 832 MET cc_start: 0.6991 (ttp) cc_final: 0.6648 (tmm) REVERT: C 1173 MET cc_start: 0.8003 (ttp) cc_final: 0.7718 (ttm) REVERT: D 171 ILE cc_start: 0.9038 (mm) cc_final: 0.8534 (tt) REVERT: D 1045 CYS cc_start: 0.8436 (m) cc_final: 0.8192 (p) REVERT: D 1085 LEU cc_start: 0.9018 (tp) cc_final: 0.8761 (mt) REVERT: D 1305 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7453 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3937 (m100) cc_final: 0.2817 (m100) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.1492 time to fit residues: 109.9855 Evaluate side-chains 322 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 29 optimal weight: 30.0000 chunk 339 optimal weight: 30.0000 chunk 190 optimal weight: 1.9990 chunk 458 optimal weight: 40.0000 chunk 478 optimal weight: 50.0000 chunk 193 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN B 816 ASN C 726 ASN D 816 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.154620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121778 restraints weight = 82964.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119926 restraints weight = 113532.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120299 restraints weight = 105290.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120187 restraints weight = 74362.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120392 restraints weight = 62056.942| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 33198 Z= 0.277 Angle : 0.738 9.552 45730 Z= 0.389 Chirality : 0.045 0.294 5584 Planarity : 0.005 0.072 5844 Dihedral : 5.903 80.200 5086 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.84 % Favored : 91.12 % Rotamer: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4640 helix: 0.71 (0.10), residues: 2614 sheet: -2.30 (0.27), residues: 316 loop : -2.53 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 477 TYR 0.038 0.002 TYR D 118 PHE 0.030 0.002 PHE C 922 TRP 0.070 0.003 TRP A 849 HIS 0.007 0.001 HIS B1161 Details of bonding type rmsd covalent geometry : bond 0.00616 (33190) covalent geometry : angle 0.73706 (45714) SS BOND : bond 0.01088 ( 8) SS BOND : angle 2.48790 ( 16) hydrogen bonds : bond 0.05025 ( 1975) hydrogen bonds : angle 4.58870 ( 5817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 832 MET cc_start: 0.7538 (ttp) cc_final: 0.6944 (tmm) REVERT: A 1173 MET cc_start: 0.7761 (ttp) cc_final: 0.7482 (ttm) REVERT: B 1335 TRP cc_start: 0.3786 (m100) cc_final: 0.2805 (m100) REVERT: C 1173 MET cc_start: 0.7734 (ttp) cc_final: 0.7468 (ttm) REVERT: D 277 LEU cc_start: 0.9101 (tp) cc_final: 0.8858 (tt) REVERT: D 1335 TRP cc_start: 0.3669 (m100) cc_final: 0.2757 (m100) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.1494 time to fit residues: 99.6584 Evaluate side-chains 295 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 178 optimal weight: 8.9990 chunk 468 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 377 optimal weight: 0.9980 chunk 280 optimal weight: 7.9990 chunk 391 optimal weight: 9.9990 chunk 474 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 321 optimal weight: 40.0000 overall best weight: 1.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN B 270 HIS B1123 ASN C 726 ASN D 270 HIS D1123 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.159279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122407 restraints weight = 82674.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117316 restraints weight = 95716.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118255 restraints weight = 77185.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119006 restraints weight = 56208.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119200 restraints weight = 47968.129| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33198 Z= 0.132 Angle : 0.582 10.845 45730 Z= 0.302 Chirality : 0.039 0.242 5584 Planarity : 0.004 0.056 5844 Dihedral : 5.406 80.490 5086 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.55 % Favored : 93.41 % Rotamer: Outliers : 0.08 % Allowed : 1.53 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4640 helix: 1.24 (0.10), residues: 2628 sheet: -2.07 (0.28), residues: 316 loop : -2.39 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1255 TYR 0.017 0.001 TYR D1083 PHE 0.028 0.001 PHE C 922 TRP 0.056 0.002 TRP B 592 HIS 0.010 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00288 (33190) covalent geometry : angle 0.58034 (45714) SS BOND : bond 0.00921 ( 8) SS BOND : angle 2.64319 ( 16) hydrogen bonds : bond 0.03921 ( 1975) hydrogen bonds : angle 3.91951 ( 5817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LEU cc_start: 0.9355 (tp) cc_final: 0.9069 (tp) REVERT: A 650 MET cc_start: 0.8317 (mtm) cc_final: 0.8106 (mtm) REVERT: A 832 MET cc_start: 0.7295 (ttp) cc_final: 0.6654 (tmm) REVERT: A 1173 MET cc_start: 0.8025 (ttp) cc_final: 0.7723 (ttm) REVERT: B 171 ILE cc_start: 0.9080 (mm) cc_final: 0.8545 (tt) REVERT: B 410 LEU cc_start: 0.9069 (tp) cc_final: 0.8817 (tt) REVERT: B 1335 TRP cc_start: 0.3875 (m100) cc_final: 0.2833 (m100) REVERT: C 138 TRP cc_start: 0.3762 (m-90) cc_final: 0.2551 (m-90) REVERT: C 650 MET cc_start: 0.8226 (mtm) cc_final: 0.8020 (mtm) REVERT: C 1173 MET cc_start: 0.8025 (ttp) cc_final: 0.7711 (ttm) REVERT: D 171 ILE cc_start: 0.9024 (mm) cc_final: 0.8519 (tt) REVERT: D 277 LEU cc_start: 0.8999 (tp) cc_final: 0.8759 (tt) REVERT: D 1085 LEU cc_start: 0.9053 (tp) cc_final: 0.8821 (mt) REVERT: D 1335 TRP cc_start: 0.3920 (m100) cc_final: 0.2882 (m100) outliers start: 2 outliers final: 0 residues processed: 401 average time/residue: 0.1464 time to fit residues: 105.9841 Evaluate side-chains 314 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 318 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 412 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 453 optimal weight: 5.9990 chunk 360 optimal weight: 20.0000 chunk 365 optimal weight: 0.1980 chunk 342 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN B 270 HIS B 656 HIS B1123 ASN C 231 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN D 270 HIS ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 HIS ** D1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.155665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.122707 restraints weight = 82844.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120597 restraints weight = 117443.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121412 restraints weight = 102415.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121242 restraints weight = 72557.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121713 restraints weight = 60334.530| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 33198 Z= 0.222 Angle : 0.687 17.134 45730 Z= 0.360 Chirality : 0.043 0.269 5584 Planarity : 0.005 0.052 5844 Dihedral : 5.682 79.373 5086 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.53 % Favored : 91.42 % Rotamer: Outliers : 0.08 % Allowed : 1.74 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4640 helix: 1.02 (0.10), residues: 2622 sheet: -2.24 (0.28), residues: 310 loop : -2.43 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1092 TYR 0.027 0.002 TYR B 657 PHE 0.033 0.002 PHE A 922 TRP 0.077 0.002 TRP C 849 HIS 0.009 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00500 (33190) covalent geometry : angle 0.68127 (45714) SS BOND : bond 0.01239 ( 8) SS BOND : angle 4.77651 ( 16) hydrogen bonds : bond 0.04634 ( 1975) hydrogen bonds : angle 4.33493 ( 5817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 832 MET cc_start: 0.7440 (ttp) cc_final: 0.6758 (tmm) REVERT: A 1173 MET cc_start: 0.7766 (ttp) cc_final: 0.7512 (ttm) REVERT: B 1335 TRP cc_start: 0.3743 (m100) cc_final: 0.2780 (m100) REVERT: C 1173 MET cc_start: 0.7738 (ttp) cc_final: 0.7493 (ttm) REVERT: D 277 LEU cc_start: 0.8916 (tp) cc_final: 0.8635 (tt) REVERT: D 1335 TRP cc_start: 0.3601 (m100) cc_final: 0.2714 (m100) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.1479 time to fit residues: 99.0387 Evaluate side-chains 304 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 398 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 322 optimal weight: 0.0570 chunk 348 optimal weight: 30.0000 chunk 357 optimal weight: 30.0000 chunk 300 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 726 ASN ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 HIS C 726 ASN ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.155400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122994 restraints weight = 82785.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121207 restraints weight = 97435.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121841 restraints weight = 90559.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121164 restraints weight = 64147.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121635 restraints weight = 56941.966| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33198 Z= 0.216 Angle : 0.674 8.992 45730 Z= 0.353 Chirality : 0.042 0.267 5584 Planarity : 0.005 0.055 5844 Dihedral : 5.750 77.507 5086 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.91 % Favored : 92.05 % Rotamer: Outliers : 0.08 % Allowed : 0.76 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 4640 helix: 0.95 (0.10), residues: 2638 sheet: -2.26 (0.28), residues: 310 loop : -2.45 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1092 TYR 0.034 0.002 TYR B 657 PHE 0.032 0.002 PHE A 922 TRP 0.066 0.002 TRP C 849 HIS 0.008 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00485 (33190) covalent geometry : angle 0.67154 (45714) SS BOND : bond 0.00535 ( 8) SS BOND : angle 2.91590 ( 16) hydrogen bonds : bond 0.04559 ( 1975) hydrogen bonds : angle 4.32892 ( 5817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 365 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 832 MET cc_start: 0.7195 (ttp) cc_final: 0.6416 (tmm) REVERT: A 1173 MET cc_start: 0.7797 (ttp) cc_final: 0.7518 (ttm) REVERT: B 277 LEU cc_start: 0.8865 (tp) cc_final: 0.8633 (tt) REVERT: B 1335 TRP cc_start: 0.3754 (m100) cc_final: 0.2758 (m100) REVERT: C 1173 MET cc_start: 0.7775 (ttp) cc_final: 0.7489 (ttm) REVERT: D 320 MET cc_start: 0.8994 (ttm) cc_final: 0.8749 (ttm) REVERT: D 1335 TRP cc_start: 0.3725 (m100) cc_final: 0.2719 (m100) outliers start: 2 outliers final: 0 residues processed: 367 average time/residue: 0.1467 time to fit residues: 96.9708 Evaluate side-chains 308 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 10 optimal weight: 2.9990 chunk 464 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 414 optimal weight: 1.9990 chunk 220 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 257 HIS C 726 ASN D 270 HIS ** D1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.156589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119421 restraints weight = 81111.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115897 restraints weight = 87665.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117020 restraints weight = 65525.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.117294 restraints weight = 47360.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117478 restraints weight = 41364.755| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33198 Z= 0.133 Angle : 0.590 9.343 45730 Z= 0.306 Chirality : 0.040 0.233 5584 Planarity : 0.004 0.047 5844 Dihedral : 5.385 76.825 5086 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.61 % Favored : 92.35 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4640 helix: 1.31 (0.10), residues: 2650 sheet: -2.05 (0.29), residues: 296 loop : -2.36 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1266 TYR 0.025 0.002 TYR C 814 PHE 0.032 0.002 PHE A 922 TRP 0.056 0.002 TRP C 849 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00292 (33190) covalent geometry : angle 0.58796 (45714) SS BOND : bond 0.00528 ( 8) SS BOND : angle 2.50259 ( 16) hydrogen bonds : bond 0.03890 ( 1975) hydrogen bonds : angle 3.93695 ( 5817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 MET cc_start: 0.7938 (ttp) cc_final: 0.7592 (ttm) REVERT: B 815 TRP cc_start: 0.8338 (t60) cc_final: 0.7598 (t60) REVERT: B 1335 TRP cc_start: 0.3724 (m100) cc_final: 0.2695 (m100) REVERT: C 320 MET cc_start: 0.2538 (tpt) cc_final: 0.2275 (tpt) REVERT: C 1173 MET cc_start: 0.8094 (ttp) cc_final: 0.7770 (ttm) REVERT: D 277 LEU cc_start: 0.8986 (tp) cc_final: 0.8734 (tt) REVERT: D 815 TRP cc_start: 0.8370 (t60) cc_final: 0.7587 (t60) REVERT: D 1335 TRP cc_start: 0.3739 (m100) cc_final: 0.2696 (m100) outliers start: 2 outliers final: 0 residues processed: 391 average time/residue: 0.1488 time to fit residues: 104.8057 Evaluate side-chains 310 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 426 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 363 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 202 optimal weight: 0.3980 chunk 261 optimal weight: 9.9990 chunk 229 optimal weight: 40.0000 chunk 406 optimal weight: 0.3980 chunk 373 optimal weight: 7.9990 chunk 314 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 726 ASN ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1123 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 = 0.4221 r_free = 0.4221 target = 0.160768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.123965 restraints weight = 82614.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120502 restraints weight = 87182.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121251 restraints weight = 69076.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121441 restraints weight = 50868.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121529 restraints weight = 43672.297| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 33198 Z= 0.111 Angle : 0.572 9.303 45730 Z= 0.291 Chirality : 0.039 0.213 5584 Planarity : 0.004 0.045 5844 Dihedral : 5.130 78.430 5086 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 0.08 % Allowed : 0.21 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 4640 helix: 1.51 (0.10), residues: 2656 sheet: -1.94 (0.29), residues: 298 loop : -2.24 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1266 TYR 0.018 0.001 TYR D 991 PHE 0.031 0.001 PHE C 922 TRP 0.048 0.002 TRP C 849 HIS 0.007 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00243 (33190) covalent geometry : angle 0.56935 (45714) SS BOND : bond 0.00542 ( 8) SS BOND : angle 3.06824 ( 16) hydrogen bonds : bond 0.03403 ( 1975) hydrogen bonds : angle 3.68118 ( 5817) =============================================================================== Job complete usr+sys time: 4621.22 seconds wall clock time: 80 minutes 12.03 seconds (4812.03 seconds total)