Starting phenix.real_space_refine on Fri Mar 6 05:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pkv_20367/03_2026/6pkv_20367.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pkv_20367/03_2026/6pkv_20367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pkv_20367/03_2026/6pkv_20367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pkv_20367/03_2026/6pkv_20367.map" model { file = "/net/cci-nas-00/data/ceres_data/6pkv_20367/03_2026/6pkv_20367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pkv_20367/03_2026/6pkv_20367.cif" } resolution = 4.3 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= 0.003 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 18092 2.51 5 N 5088 2.21 5 O 5032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 28284 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 5765 Classifications: {'peptide': 886} Incomplete info: {'truncation_to_alanine': 407} Link IDs: {'PTRANS': 24, 'TRANS': 861} Chain breaks: 16 Unresolved non-hydrogen bonds: 1501 Unresolved non-hydrogen angles: 1886 Unresolved non-hydrogen dihedrals: 1207 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLU:plan': 58, 'ASN:plan1': 16, 'PHE:plan': 18, 'ASP:plan': 28, 'TYR:plan': 11, 'ARG:plan': 36, 'GLN:plan1': 22, 'HIS:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 855 Chain: "A" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1306 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 8 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'UNK:plan-1': 22, 'ASP:plan': 5, 'GLU:plan': 6, 'HIS:plan': 3, 'ARG:plan': 11, 'GLN:plan1': 6, 'ASN:plan1': 6, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 205 Restraints were copied for chains: B, C, D Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLU A1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A1272 " occ=0.50 residue: pdb=" N VAL A1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL A1287 " 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 GLU B1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B1272 " occ=0.50 residue: pdb=" N VAL B1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL B1287 " 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 GLU C1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C1272 " occ=0.50 residue: pdb=" N VAL C1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL C1287 " 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 GLU D1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU D1272 " occ=0.50 residue: pdb=" N VAL D1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL D1287 " occ=0.50 residue: pdb=" N VAL D1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D1400 " occ=0.50 Time building chain proxies: 8.03, per 1000 atoms: 0.28 Number of scatterers: 28284 At special positions: 0 Unit cell: (148.174, 148.174, 182.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 5032 8.00 N 5088 7.00 C 18092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 65.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 40 through 49 removed outlier: 3.688A pdb=" N ASN A 47 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 177 removed outlier: 3.607A pdb=" N LYS A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.728A pdb=" N HIS A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.896A pdb=" N THR A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 426 through 439 removed outlier: 3.721A pdb=" N ARG A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.849A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.943A 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 Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.989A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 536 through 548 Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.579A pdb=" N ASN A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 620 through 639 removed outlier: 3.893A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 672 removed outlier: 3.629A pdb=" N VAL A 664 " --> pdb=" O GLN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.597A pdb=" N ILE A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 720 Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.065A pdb=" N ILE A 741 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 742 " --> pdb=" O PRO A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 808 through 833 Processing helix chain 'A' and resid 840 through 865 removed outlier: 4.008A pdb=" N PHE A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 Processing helix chain 'A' and resid 882 through 902 removed outlier: 3.543A pdb=" N GLN A 902 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 927 removed outlier: 3.716A pdb=" N ILE A 920 " --> pdb=" O CYS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 932 removed outlier: 3.791A pdb=" N ILE A 932 " --> pdb=" O ILE A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 946 removed outlier: 3.995A pdb=" N LYS A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 973 removed outlier: 3.974A pdb=" N PHE A 951 " --> pdb=" O MET A 947 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 955 " --> pdb=" O PHE A 951 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 956 " --> pdb=" O PHE A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 987 removed outlier: 3.702A pdb=" N VAL A 987 " --> pdb=" O ILE A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1065 removed outlier: 3.788A pdb=" N THR A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1092 removed outlier: 4.199A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1114 removed outlier: 4.262A pdb=" N LEU A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1154 Processing helix chain 'A' and resid 1158 through 1184 Processing helix chain 'A' and resid 1189 through 1208 Processing helix chain 'A' and resid 1270 through 1275 Processing helix chain 'A' and resid 1370 through 1381 Processing helix chain 'A' and resid 1456 through 1467 Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.688A pdb=" N ASN B 47 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 159 through 177 removed outlier: 3.608A pdb=" N LYS B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.728A pdb=" N HIS B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.895A pdb=" N THR B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 374 through 387 Processing helix chain 'B' and resid 406 through 419 Processing helix chain 'B' and resid 426 through 439 removed outlier: 3.721A pdb=" N ARG B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.849A pdb=" N ALA B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.942A pdb=" N GLY B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.989A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 536 through 548 Processing helix chain 'B' and resid 593 through 606 removed outlier: 3.578A pdb=" N ASN B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 620 through 639 removed outlier: 3.894A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 672 removed outlier: 3.630A pdb=" N VAL B 664 " --> pdb=" O GLN B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.597A pdb=" N ILE B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 720 Processing helix chain 'B' and resid 729 through 737 Processing helix chain 'B' and resid 738 through 743 removed outlier: 4.065A pdb=" N ILE B 741 " --> pdb=" O PHE B 738 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 742 " --> pdb=" O PRO B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 808 through 833 Processing helix chain 'B' and resid 840 through 865 removed outlier: 4.008A pdb=" N PHE B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 880 Processing helix chain 'B' and resid 882 through 902 removed outlier: 3.543A pdb=" N GLN B 902 " --> pdb=" O ILE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 927 removed outlier: 3.715A pdb=" N ILE B 920 " --> pdb=" O CYS B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 932 removed outlier: 3.792A pdb=" N ILE B 932 " --> pdb=" O ILE B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 946 removed outlier: 3.995A pdb=" N LYS B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET B 946 " --> pdb=" O ILE B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 973 removed outlier: 3.975A pdb=" N PHE B 951 " --> pdb=" O MET B 947 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 953 " --> pdb=" O ASP B 949 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE B 955 " --> pdb=" O PHE B 951 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 956 " --> pdb=" O PHE B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 987 removed outlier: 3.701A pdb=" N VAL B 987 " --> pdb=" O ILE B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1065 removed outlier: 3.789A pdb=" N THR B1040 " --> pdb=" O PRO B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1092 removed outlier: 4.199A pdb=" N TYR B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU B1084 " --> pdb=" O PHE B1080 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1114 removed outlier: 4.262A pdb=" N LEU B1102 " --> pdb=" O PRO B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1154 Processing helix chain 'B' and resid 1158 through 1184 Processing helix chain 'B' and resid 1189 through 1208 Processing helix chain 'B' and resid 1270 through 1275 Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1456 through 1467 Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.688A pdb=" N ASN C 47 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 48 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 159 through 177 removed outlier: 3.608A pdb=" N LYS C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 165 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.728A pdb=" N HIS C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.896A pdb=" N THR C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 406 through 419 Processing helix chain 'C' and resid 426 through 439 removed outlier: 3.721A pdb=" N ARG C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 448 removed outlier: 3.849A pdb=" N ALA C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 470 removed outlier: 3.942A 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 Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.989A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 536 through 548 Processing helix chain 'C' and resid 593 through 606 removed outlier: 3.578A pdb=" N ASN C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 620 through 639 removed outlier: 3.893A pdb=" N GLU C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 672 removed outlier: 3.629A pdb=" N VAL C 664 " --> pdb=" O GLN C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 681 Processing helix chain 'C' and resid 691 through 700 Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.597A pdb=" N ILE C 705 " --> pdb=" O ASP C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 720 Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 738 through 743 removed outlier: 4.066A pdb=" N ILE C 741 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR C 742 " --> pdb=" O PRO C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 808 through 833 Processing helix chain 'C' and resid 840 through 865 removed outlier: 4.008A pdb=" N PHE C 865 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 880 Processing helix chain 'C' and resid 882 through 902 removed outlier: 3.544A pdb=" N GLN C 902 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 927 removed outlier: 3.715A pdb=" N ILE C 920 " --> pdb=" O CYS C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 932 removed outlier: 3.792A pdb=" N ILE C 932 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 946 removed outlier: 3.996A pdb=" N LYS C 939 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 943 " --> pdb=" O LYS C 939 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 946 " --> pdb=" O ILE C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 973 removed outlier: 3.975A pdb=" N PHE C 951 " --> pdb=" O MET C 947 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE C 955 " --> pdb=" O PHE C 951 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 956 " --> pdb=" O PHE C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 987 removed outlier: 3.702A pdb=" N VAL C 987 " --> pdb=" O ILE C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1065 removed outlier: 3.788A pdb=" N THR C1040 " --> pdb=" O PRO C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1092 removed outlier: 4.199A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU C1084 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1096 through 1114 removed outlier: 4.262A pdb=" N LEU C1102 " --> pdb=" O PRO C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1154 Processing helix chain 'C' and resid 1158 through 1184 Processing helix chain 'C' and resid 1189 through 1208 Processing helix chain 'C' and resid 1270 through 1275 Processing helix chain 'C' and resid 1370 through 1381 Processing helix chain 'C' and resid 1456 through 1467 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.688A pdb=" N ASN D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 48 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 159 through 177 removed outlier: 3.606A pdb=" N LYS D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 165 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.728A pdb=" N HIS D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.897A pdb=" N THR D 315 " --> pdb=" O GLY D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 342 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 406 through 419 Processing helix chain 'D' and resid 426 through 439 removed outlier: 3.721A pdb=" N ARG D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 448 removed outlier: 3.849A pdb=" N ALA D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.943A pdb=" N GLY D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 492 through 502 removed outlier: 3.989A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 536 through 548 Processing helix chain 'D' and resid 593 through 606 removed outlier: 3.578A pdb=" N ASN D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 618 Processing helix chain 'D' and resid 620 through 639 removed outlier: 3.894A pdb=" N GLU D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 672 removed outlier: 3.630A pdb=" N VAL D 664 " --> pdb=" O GLN D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 681 Processing helix chain 'D' and resid 691 through 700 Processing helix chain 'D' and resid 701 through 706 removed outlier: 3.596A pdb=" N ILE D 705 " --> pdb=" O ASP D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 720 Processing helix chain 'D' and resid 729 through 737 Processing helix chain 'D' and resid 738 through 743 removed outlier: 4.065A pdb=" N ILE D 741 " --> pdb=" O PHE D 738 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 742 " --> pdb=" O PRO D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'D' and resid 799 through 807 Processing helix chain 'D' and resid 808 through 833 Processing helix chain 'D' and resid 840 through 865 removed outlier: 4.008A pdb=" N PHE D 865 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 880 Processing helix chain 'D' and resid 882 through 902 removed outlier: 3.544A pdb=" N GLN D 902 " --> pdb=" O ILE D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 927 removed outlier: 3.715A pdb=" N ILE D 920 " --> pdb=" O CYS D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 932 removed outlier: 3.791A pdb=" N ILE D 932 " --> pdb=" O ILE D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 935 through 946 removed outlier: 3.995A pdb=" N LYS D 939 " --> pdb=" O THR D 935 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 943 " --> pdb=" O LYS D 939 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET D 946 " --> pdb=" O ILE D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 973 removed outlier: 3.974A pdb=" N PHE D 951 " --> pdb=" O MET D 947 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 953 " --> pdb=" O ASP D 949 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET D 954 " --> pdb=" O LEU D 950 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D 955 " --> pdb=" O PHE D 951 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU D 956 " --> pdb=" O PHE D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 987 removed outlier: 3.702A pdb=" N VAL D 987 " --> pdb=" O ILE D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1065 removed outlier: 3.789A pdb=" N THR D1040 " --> pdb=" O PRO D1036 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1092 removed outlier: 4.199A pdb=" N TYR D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU D1084 " --> pdb=" O PHE D1080 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1114 removed outlier: 4.262A pdb=" N LEU D1102 " --> pdb=" O PRO D1098 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1154 Processing helix chain 'D' and resid 1158 through 1184 Processing helix chain 'D' and resid 1189 through 1208 Processing helix chain 'D' and resid 1270 through 1275 Processing helix chain 'D' and resid 1370 through 1381 Processing helix chain 'D' and resid 1456 through 1467 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.871A pdb=" N LYS A 117 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU A 262 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 119 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 179 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE A 215 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 181 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL A 217 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 145 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU A 182 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 147 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY A 184 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N VAL A 149 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL A 304 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER A 148 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N VAL A 327 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 8.391A pdb=" N VAL A1411 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR A1399 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A1413 " --> pdb=" O LYS A1397 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS A1397 " --> pdb=" O THR A1413 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A1415 " --> pdb=" O VAL A1395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 6.053A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1346 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.871A pdb=" N LYS B 117 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 262 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 119 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 179 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE B 215 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE B 181 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 217 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 145 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 182 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 147 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY B 184 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N VAL B 149 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 146 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL B 304 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER B 148 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N VAL B 327 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1361 through 1362 removed outlier: 8.391A pdb=" N VAL B1411 " --> pdb=" O TYR B1399 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR B1399 " --> pdb=" O VAL B1411 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B1413 " --> pdb=" O LYS B1397 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS B1397 " --> pdb=" O THR B1413 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B1415 " --> pdb=" O VAL B1395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1361 through 1362 removed outlier: 6.053A pdb=" N PHE B1332 " --> pdb=" O LEU B1346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B1346 " --> pdb=" O PHE B1332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.871A pdb=" N LYS C 117 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU C 262 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 119 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA C 179 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE C 215 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE C 181 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL C 217 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU C 145 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU C 182 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY C 184 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N VAL C 149 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL C 304 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER C 148 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N VAL C 327 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 8.391A pdb=" N VAL C1411 " --> pdb=" O TYR C1399 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR C1399 " --> pdb=" O VAL C1411 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1413 " --> pdb=" O LYS C1397 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS C1397 " --> pdb=" O THR C1413 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C1415 " --> pdb=" O VAL C1395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 6.053A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C1346 " --> pdb=" O PHE C1332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 104 through 106 removed outlier: 6.872A pdb=" N LYS D 117 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU D 262 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 119 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA D 179 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE D 215 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE D 181 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL D 217 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU D 145 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU D 182 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY D 184 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N VAL D 149 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU D 146 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL D 304 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER D 148 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N VAL D 327 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 1361 through 1362 removed outlier: 8.391A pdb=" N VAL D1411 " --> pdb=" O TYR D1399 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR D1399 " --> pdb=" O VAL D1411 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR D1413 " --> pdb=" O LYS D1397 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS D1397 " --> pdb=" O THR D1413 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D1415 " --> pdb=" O VAL D1395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 1361 through 1362 removed outlier: 6.053A pdb=" N PHE D1332 " --> pdb=" O LEU D1346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D1346 " --> pdb=" O PHE D1332 " (cutoff:3.500A) 2017 hydrogen bonds defined for protein. 5943 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: 5.16 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9481 1.34 - 1.46: 5813 1.46 - 1.58: 13462 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 28844 Sorted by residual: bond pdb=" C SER D1281 " pdb=" N PRO D1282 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.59e+00 bond pdb=" C SER A1281 " pdb=" N PRO A1282 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.42e+00 bond pdb=" C SER C1281 " pdb=" N PRO C1282 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.36e+00 bond pdb=" C SER B1281 " pdb=" N PRO B1282 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.36e+00 bond pdb=" C PHE B 738 " pdb=" N PRO B 739 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.29e+00 ... (remaining 28839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 38632 2.29 - 4.59: 887 4.59 - 6.88: 105 6.88 - 9.18: 40 9.18 - 11.47: 8 Bond angle restraints: 39672 Sorted by residual: angle pdb=" N PRO B 504 " pdb=" CA PRO B 504 " pdb=" C PRO B 504 " ideal model delta sigma weight residual 112.47 123.20 -10.73 2.06e+00 2.36e-01 2.71e+01 angle pdb=" N PRO A 504 " pdb=" CA PRO A 504 " pdb=" C PRO A 504 " ideal model delta sigma weight residual 112.47 123.18 -10.71 2.06e+00 2.36e-01 2.70e+01 angle pdb=" N PRO C 504 " pdb=" CA PRO C 504 " pdb=" C PRO C 504 " ideal model delta sigma weight residual 112.47 123.18 -10.71 2.06e+00 2.36e-01 2.70e+01 angle pdb=" N PRO D 504 " pdb=" CA PRO D 504 " pdb=" C PRO D 504 " ideal model delta sigma weight residual 112.47 123.14 -10.67 2.06e+00 2.36e-01 2.68e+01 angle pdb=" N SER B 505 " pdb=" CA SER B 505 " pdb=" C SER B 505 " ideal model delta sigma weight residual 107.49 116.18 -8.69 1.74e+00 3.30e-01 2.50e+01 ... (remaining 39667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.05: 15326 12.05 - 24.11: 982 24.11 - 36.16: 140 36.16 - 48.21: 36 48.21 - 60.27: 4 Dihedral angle restraints: 16488 sinusoidal: 3888 harmonic: 12600 Sorted by residual: dihedral pdb=" CA ASP D 620 " pdb=" C ASP D 620 " pdb=" N CYS D 621 " pdb=" CA CYS D 621 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 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 -150.06 -29.94 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASP C 620 " pdb=" C ASP C 620 " pdb=" N CYS C 621 " pdb=" CA CYS C 621 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 16485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4128 0.065 - 0.130: 617 0.130 - 0.194: 83 0.194 - 0.259: 20 0.259 - 0.324: 4 Chirality restraints: 4852 Sorted by residual: chirality pdb=" CA PRO B 504 " pdb=" N PRO B 504 " pdb=" C PRO B 504 " pdb=" CB PRO B 504 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PRO A 504 " pdb=" N PRO A 504 " pdb=" C PRO A 504 " pdb=" CB PRO A 504 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PRO C 504 " pdb=" N PRO C 504 " pdb=" C PRO C 504 " pdb=" CB PRO C 504 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 4849 not shown) Planarity restraints: 5124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 503 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C LEU D 503 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU D 503 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO D 504 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 503 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LEU B 503 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU B 503 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO B 504 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 503 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LEU A 503 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU A 503 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO A 504 " -0.019 2.00e-02 2.50e+03 ... (remaining 5121 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 8993 2.83 - 3.35: 26537 3.35 - 3.86: 44867 3.86 - 4.38: 45083 4.38 - 4.90: 77837 Nonbonded interactions: 203317 Sorted by model distance: nonbonded pdb=" OH TYR D1283 " pdb=" OD2 ASP D1407 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR C1283 " pdb=" OD2 ASP C1407 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR B1283 " pdb=" OD2 ASP B1407 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A1283 " pdb=" OD2 ASP A1407 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR B 742 " pdb=" O CYS B 798 " model vdw 2.388 3.040 ... (remaining 203312 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.640 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: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28844 Z= 0.238 Angle : 0.857 11.471 39672 Z= 0.474 Chirality : 0.050 0.324 4852 Planarity : 0.007 0.054 5124 Dihedral : 8.985 60.268 8208 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.11), residues: 4060 helix: -1.82 (0.08), residues: 2508 sheet: -2.11 (0.25), residues: 352 loop : -2.96 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 619 TYR 0.024 0.003 TYR B1259 PHE 0.025 0.002 PHE D1280 TRP 0.051 0.003 TRP C 592 HIS 0.011 0.002 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00495 (28844) covalent geometry : angle 0.85746 (39672) hydrogen bonds : bond 0.13854 ( 2009) hydrogen bonds : angle 5.98280 ( 5943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.929 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 286 SER cc_start: 0.8980 (t) cc_final: 0.8757 (p) REVERT: A 662 ILE cc_start: 0.9587 (pt) cc_final: 0.9329 (mt) REVERT: A 679 LEU cc_start: 0.9209 (mp) cc_final: 0.8957 (tt) REVERT: A 913 VAL cc_start: 0.8907 (t) cc_final: 0.8707 (p) REVERT: A 922 PHE cc_start: 0.8656 (m-80) cc_final: 0.8170 (m-80) REVERT: B 180 TRP cc_start: 0.8353 (m-10) cc_final: 0.8152 (m-10) REVERT: B 286 SER cc_start: 0.8919 (t) cc_final: 0.8703 (p) REVERT: B 662 ILE cc_start: 0.9632 (pt) cc_final: 0.9305 (mt) REVERT: B 922 PHE cc_start: 0.8704 (m-80) cc_final: 0.8150 (m-80) REVERT: C 180 TRP cc_start: 0.8357 (m-10) cc_final: 0.8153 (m-10) REVERT: C 286 SER cc_start: 0.8919 (t) cc_final: 0.8702 (p) REVERT: C 662 ILE cc_start: 0.9632 (pt) cc_final: 0.9300 (mt) REVERT: C 922 PHE cc_start: 0.8707 (m-80) cc_final: 0.8157 (m-80) REVERT: D 180 TRP cc_start: 0.8352 (m-10) cc_final: 0.8151 (m-10) REVERT: D 286 SER cc_start: 0.8922 (t) cc_final: 0.8714 (p) REVERT: D 662 ILE cc_start: 0.9631 (pt) cc_final: 0.9297 (mt) REVERT: D 922 PHE cc_start: 0.8703 (m-80) cc_final: 0.8156 (m-80) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.1490 time to fit residues: 105.5000 Evaluate side-chains 266 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 40.0000 chunk 424 optimal weight: 40.0000 chunk 155 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 193 HIS A 656 HIS A 707 HIS A1081 GLN A1104 HIS A1164 HIS B 187 HIS B 193 HIS B 656 HIS B 707 HIS B1081 GLN B1104 HIS B1164 HIS C 187 HIS C 193 HIS C 656 HIS C 707 HIS C1081 GLN C1104 HIS C1164 HIS D 187 HIS D 193 HIS D 707 HIS D1081 GLN D1104 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.105724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.084904 restraints weight = 160185.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082052 restraints weight = 134958.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082546 restraints weight = 119608.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082522 restraints weight = 95016.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082596 restraints weight = 90463.432| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28844 Z= 0.127 Angle : 0.540 7.089 39672 Z= 0.288 Chirality : 0.037 0.151 4852 Planarity : 0.005 0.042 5124 Dihedral : 4.999 22.494 4412 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4060 helix: 0.42 (0.10), residues: 2556 sheet: -1.63 (0.27), residues: 348 loop : -2.65 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1092 TYR 0.016 0.002 TYR C1259 PHE 0.012 0.001 PHE A 599 TRP 0.026 0.002 TRP A 592 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00263 (28844) covalent geometry : angle 0.53972 (39672) hydrogen bonds : bond 0.03538 ( 2009) hydrogen bonds : angle 4.05522 ( 5943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 SER cc_start: 0.9117 (t) cc_final: 0.8899 (p) REVERT: A 922 PHE cc_start: 0.8519 (m-80) cc_final: 0.7938 (m-80) REVERT: A 1173 MET cc_start: 0.8574 (ttm) cc_final: 0.8230 (tpp) REVERT: B 180 TRP cc_start: 0.8372 (m-10) cc_final: 0.8114 (m-10) REVERT: B 286 SER cc_start: 0.9126 (t) cc_final: 0.8875 (p) REVERT: B 922 PHE cc_start: 0.8688 (m-80) cc_final: 0.7990 (m-80) REVERT: C 180 TRP cc_start: 0.8364 (m-10) cc_final: 0.8110 (m-10) REVERT: C 286 SER cc_start: 0.9112 (t) cc_final: 0.8867 (p) REVERT: C 922 PHE cc_start: 0.8690 (m-80) cc_final: 0.7991 (m-80) REVERT: D 180 TRP cc_start: 0.8377 (m-10) cc_final: 0.8109 (m-10) REVERT: D 286 SER cc_start: 0.9123 (t) cc_final: 0.8868 (p) REVERT: D 922 PHE cc_start: 0.8692 (m-80) cc_final: 0.7981 (m-80) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1345 time to fit residues: 72.6550 Evaluate side-chains 238 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 276 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 380 optimal weight: 9.9990 chunk 209 optimal weight: 50.0000 chunk 269 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 174 optimal weight: 50.0000 chunk 221 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 410 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 883 ASN B1081 GLN C 883 ASN D 656 HIS D 883 ASN D1081 GLN D1164 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.096708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071921 restraints weight = 142640.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069306 restraints weight = 110565.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069529 restraints weight = 94629.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069693 restraints weight = 83362.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069747 restraints weight = 76082.611| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28844 Z= 0.231 Angle : 0.642 8.981 39672 Z= 0.340 Chirality : 0.039 0.156 4852 Planarity : 0.005 0.042 5124 Dihedral : 4.924 22.372 4412 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4060 helix: 1.24 (0.10), residues: 2556 sheet: -1.46 (0.27), residues: 348 loop : -2.40 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1162 TYR 0.018 0.002 TYR B 131 PHE 0.024 0.002 PHE A 745 TRP 0.028 0.002 TRP A 592 HIS 0.008 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00487 (28844) covalent geometry : angle 0.64193 (39672) hydrogen bonds : bond 0.04147 ( 2009) hydrogen bonds : angle 4.21593 ( 5943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 SER cc_start: 0.9271 (t) cc_final: 0.9006 (p) REVERT: A 922 PHE cc_start: 0.8419 (m-80) cc_final: 0.7995 (m-80) REVERT: A 1173 MET cc_start: 0.8645 (ttm) cc_final: 0.8234 (mmm) REVERT: B 180 TRP cc_start: 0.8471 (m-10) cc_final: 0.8139 (m-10) REVERT: B 286 SER cc_start: 0.9247 (t) cc_final: 0.8995 (p) REVERT: B 922 PHE cc_start: 0.8698 (m-80) cc_final: 0.7999 (m-80) REVERT: B 1173 MET cc_start: 0.8394 (mmm) cc_final: 0.8055 (mmm) REVERT: C 180 TRP cc_start: 0.8474 (m-10) cc_final: 0.8150 (m-10) REVERT: C 286 SER cc_start: 0.9236 (t) cc_final: 0.8991 (p) REVERT: C 922 PHE cc_start: 0.8689 (m-80) cc_final: 0.7991 (m-80) REVERT: C 1173 MET cc_start: 0.8407 (mmm) cc_final: 0.8176 (mmm) REVERT: D 180 TRP cc_start: 0.8484 (m-10) cc_final: 0.8150 (m-10) REVERT: D 286 SER cc_start: 0.9253 (t) cc_final: 0.9000 (p) REVERT: D 922 PHE cc_start: 0.8697 (m-80) cc_final: 0.7988 (m-80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1352 time to fit residues: 58.4836 Evaluate side-chains 214 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 199 optimal weight: 0.0870 chunk 169 optimal weight: 8.9990 chunk 347 optimal weight: 20.0000 chunk 300 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 420 optimal weight: 50.0000 chunk 379 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 216 optimal weight: 30.0000 chunk 368 optimal weight: 6.9990 chunk 357 optimal weight: 2.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.098189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.073324 restraints weight = 142323.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070945 restraints weight = 102801.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.071138 restraints weight = 91472.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071326 restraints weight = 79838.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071319 restraints weight = 71574.697| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28844 Z= 0.149 Angle : 0.536 6.973 39672 Z= 0.284 Chirality : 0.038 0.154 4852 Planarity : 0.004 0.039 5124 Dihedral : 4.502 22.633 4412 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 4060 helix: 1.64 (0.10), residues: 2572 sheet: -1.25 (0.30), residues: 312 loop : -2.42 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 440 TYR 0.015 0.001 TYR B1259 PHE 0.012 0.001 PHE B1280 TRP 0.053 0.002 TRP A 592 HIS 0.006 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00318 (28844) covalent geometry : angle 0.53555 (39672) hydrogen bonds : bond 0.03403 ( 2009) hydrogen bonds : angle 3.78463 ( 5943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 SER cc_start: 0.9194 (t) cc_final: 0.8903 (p) REVERT: A 922 PHE cc_start: 0.8402 (m-80) cc_final: 0.7972 (m-80) REVERT: A 1173 MET cc_start: 0.8578 (ttm) cc_final: 0.8260 (mmm) REVERT: B 180 TRP cc_start: 0.8451 (m-10) cc_final: 0.8173 (m-10) REVERT: B 286 SER cc_start: 0.9160 (t) cc_final: 0.8861 (p) REVERT: B 922 PHE cc_start: 0.8665 (m-80) cc_final: 0.7970 (m-80) REVERT: C 180 TRP cc_start: 0.8452 (m-10) cc_final: 0.8177 (m-10) REVERT: C 286 SER cc_start: 0.9167 (t) cc_final: 0.8867 (p) REVERT: C 922 PHE cc_start: 0.8648 (m-80) cc_final: 0.7984 (m-80) REVERT: D 180 TRP cc_start: 0.8459 (m-10) cc_final: 0.8174 (m-10) REVERT: D 286 SER cc_start: 0.9169 (t) cc_final: 0.8868 (p) REVERT: D 922 PHE cc_start: 0.8653 (m-80) cc_final: 0.7952 (m-80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1373 time to fit residues: 62.6660 Evaluate side-chains 224 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 59 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 405 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 249 optimal weight: 9.9990 chunk 210 optimal weight: 50.0000 chunk 164 optimal weight: 3.9990 chunk 391 optimal weight: 30.0000 chunk 147 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.102319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080881 restraints weight = 159654.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.078269 restraints weight = 130726.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.078491 restraints weight = 126882.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078592 restraints weight = 107432.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078670 restraints weight = 94054.091| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28844 Z= 0.174 Angle : 0.564 7.536 39672 Z= 0.296 Chirality : 0.038 0.156 4852 Planarity : 0.004 0.056 5124 Dihedral : 4.463 22.816 4412 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 4060 helix: 1.85 (0.10), residues: 2580 sheet: -1.22 (0.30), residues: 312 loop : -2.37 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 925 TYR 0.015 0.002 TYR C1259 PHE 0.014 0.002 PHE A1280 TRP 0.040 0.002 TRP A 592 HIS 0.008 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00367 (28844) covalent geometry : angle 0.56418 (39672) hydrogen bonds : bond 0.03519 ( 2009) hydrogen bonds : angle 3.84030 ( 5943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.002 Fit side-chains REVERT: A 215 ILE cc_start: 0.9258 (mp) cc_final: 0.9058 (mt) REVERT: A 286 SER cc_start: 0.9284 (t) cc_final: 0.9032 (p) REVERT: A 922 PHE cc_start: 0.8451 (m-80) cc_final: 0.8102 (m-80) REVERT: A 1173 MET cc_start: 0.8908 (ttm) cc_final: 0.8362 (mmm) REVERT: B 180 TRP cc_start: 0.8483 (m-10) cc_final: 0.8222 (m-10) REVERT: B 286 SER cc_start: 0.9270 (t) cc_final: 0.9010 (p) REVERT: B 922 PHE cc_start: 0.8658 (m-80) cc_final: 0.8254 (m-80) REVERT: B 1173 MET cc_start: 0.8488 (mmm) cc_final: 0.8155 (mmm) REVERT: C 180 TRP cc_start: 0.8497 (m-10) cc_final: 0.8236 (m-10) REVERT: C 286 SER cc_start: 0.9264 (t) cc_final: 0.9002 (p) REVERT: C 922 PHE cc_start: 0.8645 (m-80) cc_final: 0.7922 (m-80) REVERT: D 180 TRP cc_start: 0.8482 (m-10) cc_final: 0.8213 (m-10) REVERT: D 286 SER cc_start: 0.9270 (t) cc_final: 0.9009 (p) REVERT: D 922 PHE cc_start: 0.8640 (m-80) cc_final: 0.8223 (m-80) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1294 time to fit residues: 56.0803 Evaluate side-chains 210 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 174 optimal weight: 40.0000 chunk 352 optimal weight: 0.9990 chunk 12 optimal weight: 40.0000 chunk 331 optimal weight: 3.9990 chunk 182 optimal weight: 0.0770 chunk 209 optimal weight: 1.9990 chunk 127 optimal weight: 30.0000 chunk 425 optimal weight: 50.0000 chunk 361 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 408 optimal weight: 0.8980 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.105305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084564 restraints weight = 159572.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081575 restraints weight = 128385.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081894 restraints weight = 128886.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.082177 restraints weight = 105295.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.082183 restraints weight = 91265.689| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28844 Z= 0.093 Angle : 0.478 6.799 39672 Z= 0.246 Chirality : 0.036 0.144 4852 Planarity : 0.004 0.060 5124 Dihedral : 4.071 23.906 4412 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 4060 helix: 2.16 (0.10), residues: 2580 sheet: -0.81 (0.31), residues: 292 loop : -2.34 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 925 TYR 0.015 0.001 TYR A1259 PHE 0.007 0.001 PHE B1280 TRP 0.021 0.001 TRP D 592 HIS 0.003 0.001 HIS C1164 Details of bonding type rmsd covalent geometry : bond 0.00192 (28844) covalent geometry : angle 0.47823 (39672) hydrogen bonds : bond 0.02758 ( 2009) hydrogen bonds : angle 3.38701 ( 5943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.961 Fit side-chains REVERT: A 286 SER cc_start: 0.9196 (t) cc_final: 0.8920 (p) REVERT: A 922 PHE cc_start: 0.8460 (m-80) cc_final: 0.8201 (m-80) REVERT: A 1173 MET cc_start: 0.8562 (ttm) cc_final: 0.8224 (mmm) REVERT: B 180 TRP cc_start: 0.8400 (m-10) cc_final: 0.8147 (m-10) REVERT: B 286 SER cc_start: 0.9163 (t) cc_final: 0.8877 (p) REVERT: B 827 PHE cc_start: 0.8154 (t80) cc_final: 0.7829 (t80) REVERT: B 922 PHE cc_start: 0.8737 (m-80) cc_final: 0.8109 (m-80) REVERT: C 180 TRP cc_start: 0.8397 (m-10) cc_final: 0.8149 (m-10) REVERT: C 286 SER cc_start: 0.9156 (t) cc_final: 0.8869 (p) REVERT: C 827 PHE cc_start: 0.8130 (t80) cc_final: 0.7841 (t80) REVERT: C 922 PHE cc_start: 0.8709 (m-80) cc_final: 0.8050 (m-80) REVERT: D 180 TRP cc_start: 0.8359 (m-10) cc_final: 0.8106 (m-10) REVERT: D 286 SER cc_start: 0.9160 (t) cc_final: 0.8872 (p) REVERT: D 827 PHE cc_start: 0.8135 (t80) cc_final: 0.7840 (t80) REVERT: D 922 PHE cc_start: 0.8710 (m-80) cc_final: 0.8081 (m-80) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1285 time to fit residues: 62.6631 Evaluate side-chains 225 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 244 optimal weight: 0.0670 chunk 359 optimal weight: 8.9990 chunk 427 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 157 optimal weight: 0.2980 overall best weight: 3.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.103986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082642 restraints weight = 159264.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080021 restraints weight = 122551.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.080347 restraints weight = 127462.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080415 restraints weight = 99959.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080732 restraints weight = 94375.929| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28844 Z= 0.124 Angle : 0.503 6.586 39672 Z= 0.260 Chirality : 0.037 0.149 4852 Planarity : 0.004 0.045 5124 Dihedral : 4.037 23.348 4412 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.05 % Allowed : 1.50 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.14), residues: 4060 helix: 2.28 (0.10), residues: 2580 sheet: -1.14 (0.29), residues: 312 loop : -2.27 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 925 TYR 0.017 0.001 TYR C1142 PHE 0.014 0.001 PHE D1280 TRP 0.026 0.001 TRP A 592 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00264 (28844) covalent geometry : angle 0.50306 (39672) hydrogen bonds : bond 0.02976 ( 2009) hydrogen bonds : angle 3.43133 ( 5943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.716 Fit side-chains REVERT: A 286 SER cc_start: 0.9101 (t) cc_final: 0.8850 (p) REVERT: A 922 PHE cc_start: 0.8525 (m-80) cc_final: 0.8255 (m-80) REVERT: A 1173 MET cc_start: 0.8666 (ttm) cc_final: 0.8095 (mmm) REVERT: B 286 SER cc_start: 0.9086 (t) cc_final: 0.8821 (p) REVERT: B 827 PHE cc_start: 0.8224 (t80) cc_final: 0.7893 (t80) REVERT: B 922 PHE cc_start: 0.8748 (m-80) cc_final: 0.8047 (m-80) REVERT: C 286 SER cc_start: 0.9064 (t) cc_final: 0.8809 (p) REVERT: C 922 PHE cc_start: 0.8718 (m-80) cc_final: 0.7968 (m-80) REVERT: D 286 SER cc_start: 0.9071 (t) cc_final: 0.8813 (p) REVERT: D 922 PHE cc_start: 0.8720 (m-80) cc_final: 0.7994 (m-80) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.1256 time to fit residues: 57.2269 Evaluate side-chains 221 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 328 optimal weight: 9.9990 chunk 206 optimal weight: 40.0000 chunk 410 optimal weight: 5.9990 chunk 414 optimal weight: 50.0000 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.101365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079978 restraints weight = 159795.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077264 restraints weight = 131125.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077652 restraints weight = 122271.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077740 restraints weight = 104887.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077793 restraints weight = 92711.592| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28844 Z= 0.208 Angle : 0.607 8.803 39672 Z= 0.318 Chirality : 0.039 0.221 4852 Planarity : 0.004 0.056 5124 Dihedral : 4.438 22.601 4412 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 4060 helix: 2.00 (0.10), residues: 2592 sheet: -1.25 (0.29), residues: 304 loop : -2.30 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 925 TYR 0.016 0.002 TYR B 131 PHE 0.016 0.002 PHE A 745 TRP 0.039 0.002 TRP A 592 HIS 0.008 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00439 (28844) covalent geometry : angle 0.60693 (39672) hydrogen bonds : bond 0.03765 ( 2009) hydrogen bonds : angle 3.94162 ( 5943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.078 Fit side-chains REVERT: A 286 SER cc_start: 0.9301 (t) cc_final: 0.9078 (p) REVERT: A 922 PHE cc_start: 0.8517 (m-80) cc_final: 0.8123 (m-80) REVERT: A 1173 MET cc_start: 0.8742 (ttm) cc_final: 0.8432 (mmm) REVERT: B 286 SER cc_start: 0.9312 (t) cc_final: 0.9068 (p) REVERT: B 922 PHE cc_start: 0.8759 (m-80) cc_final: 0.8086 (m-80) REVERT: C 286 SER cc_start: 0.9292 (t) cc_final: 0.9058 (p) REVERT: C 922 PHE cc_start: 0.8750 (m-80) cc_final: 0.8066 (m-80) REVERT: D 286 SER cc_start: 0.9298 (t) cc_final: 0.9062 (p) REVERT: D 922 PHE cc_start: 0.8765 (m-80) cc_final: 0.8105 (m-80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1287 time to fit residues: 54.6578 Evaluate side-chains 195 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 371 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 HIS C 259 HIS D 259 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.104952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085159 restraints weight = 156618.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083215 restraints weight = 144587.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083549 restraints weight = 147307.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083484 restraints weight = 110441.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083715 restraints weight = 96907.086| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28844 Z= 0.107 Angle : 0.497 6.571 39672 Z= 0.258 Chirality : 0.037 0.145 4852 Planarity : 0.004 0.036 5124 Dihedral : 4.121 22.828 4412 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 4060 helix: 2.24 (0.10), residues: 2584 sheet: -1.19 (0.29), residues: 312 loop : -2.27 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 925 TYR 0.013 0.001 TYR A1259 PHE 0.011 0.001 PHE D1280 TRP 0.050 0.002 TRP D 592 HIS 0.007 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00227 (28844) covalent geometry : angle 0.49742 (39672) hydrogen bonds : bond 0.02923 ( 2009) hydrogen bonds : angle 3.42916 ( 5943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.968 Fit side-chains REVERT: A 286 SER cc_start: 0.9072 (t) cc_final: 0.8865 (p) REVERT: A 922 PHE cc_start: 0.8496 (m-80) cc_final: 0.8201 (m-80) REVERT: A 1173 MET cc_start: 0.8557 (ttm) cc_final: 0.8230 (mmm) REVERT: B 286 SER cc_start: 0.9058 (t) cc_final: 0.8843 (p) REVERT: B 802 LEU cc_start: 0.9315 (tt) cc_final: 0.9084 (mm) REVERT: B 922 PHE cc_start: 0.8679 (m-80) cc_final: 0.7885 (m-80) REVERT: C 286 SER cc_start: 0.9056 (t) cc_final: 0.8846 (p) REVERT: C 802 LEU cc_start: 0.9302 (tt) cc_final: 0.9063 (mm) REVERT: C 922 PHE cc_start: 0.8672 (m-80) cc_final: 0.7864 (m-80) REVERT: D 286 SER cc_start: 0.9050 (t) cc_final: 0.8836 (p) REVERT: D 802 LEU cc_start: 0.9302 (tt) cc_final: 0.9059 (mm) REVERT: D 922 PHE cc_start: 0.8662 (m-80) cc_final: 0.7882 (m-80) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1288 time to fit residues: 58.3241 Evaluate side-chains 218 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 144 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 329 optimal weight: 0.3980 chunk 260 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 360 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 345 optimal weight: 50.0000 chunk 269 optimal weight: 20.0000 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.106289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085967 restraints weight = 156232.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083491 restraints weight = 134076.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083867 restraints weight = 118659.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084555 restraints weight = 94750.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084484 restraints weight = 78175.340| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28844 Z= 0.092 Angle : 0.473 6.582 39672 Z= 0.242 Chirality : 0.036 0.145 4852 Planarity : 0.003 0.035 5124 Dihedral : 3.801 23.769 4412 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.14), residues: 4060 helix: 2.54 (0.10), residues: 2580 sheet: -1.03 (0.29), residues: 312 loop : -2.18 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 925 TYR 0.014 0.001 TYR A1259 PHE 0.010 0.001 PHE D1280 TRP 0.046 0.001 TRP A 592 HIS 0.003 0.000 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00196 (28844) covalent geometry : angle 0.47281 (39672) hydrogen bonds : bond 0.02573 ( 2009) hydrogen bonds : angle 3.22269 ( 5943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.962 Fit side-chains REVERT: A 286 SER cc_start: 0.9056 (t) cc_final: 0.8852 (p) REVERT: A 827 PHE cc_start: 0.8285 (t80) cc_final: 0.7978 (t80) REVERT: A 922 PHE cc_start: 0.8495 (m-80) cc_final: 0.7785 (m-80) REVERT: A 1173 MET cc_start: 0.8514 (ttm) cc_final: 0.8275 (mmm) REVERT: B 286 SER cc_start: 0.9031 (t) cc_final: 0.8828 (p) REVERT: B 802 LEU cc_start: 0.9323 (tt) cc_final: 0.9077 (mm) REVERT: B 827 PHE cc_start: 0.8318 (t80) cc_final: 0.8035 (t80) REVERT: B 922 PHE cc_start: 0.8636 (m-80) cc_final: 0.7919 (m-80) REVERT: C 286 SER cc_start: 0.9028 (t) cc_final: 0.8817 (p) REVERT: C 802 LEU cc_start: 0.9320 (tt) cc_final: 0.9071 (mm) REVERT: C 827 PHE cc_start: 0.8313 (t80) cc_final: 0.8038 (t80) REVERT: C 922 PHE cc_start: 0.8679 (m-80) cc_final: 0.7957 (m-80) REVERT: C 1143 MET cc_start: 0.8567 (tpp) cc_final: 0.8074 (tpp) REVERT: D 286 SER cc_start: 0.9031 (t) cc_final: 0.8824 (p) REVERT: D 827 PHE cc_start: 0.8314 (t80) cc_final: 0.8037 (t80) REVERT: D 922 PHE cc_start: 0.8622 (m-80) cc_final: 0.7908 (m-80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1306 time to fit residues: 63.7923 Evaluate side-chains 228 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 188 optimal weight: 4.9990 chunk 339 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 162 optimal weight: 30.0000 chunk 415 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 159 optimal weight: 0.0070 chunk 367 optimal weight: 3.9990 chunk 311 optimal weight: 40.0000 chunk 414 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS A1057 ASN B1057 ASN C1057 ASN D1057 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.105535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085526 restraints weight = 156499.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082811 restraints weight = 141799.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083433 restraints weight = 123454.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083431 restraints weight = 93155.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083496 restraints weight = 90215.238| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28844 Z= 0.103 Angle : 0.478 9.277 39672 Z= 0.246 Chirality : 0.036 0.144 4852 Planarity : 0.003 0.035 5124 Dihedral : 3.793 23.494 4412 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.14), residues: 4060 helix: 2.58 (0.10), residues: 2584 sheet: -0.94 (0.28), residues: 312 loop : -2.18 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 925 TYR 0.014 0.001 TYR A1259 PHE 0.010 0.001 PHE A1280 TRP 0.043 0.001 TRP B 592 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00222 (28844) covalent geometry : angle 0.47849 (39672) hydrogen bonds : bond 0.02653 ( 2009) hydrogen bonds : angle 3.22119 ( 5943) =============================================================================== Job complete usr+sys time: 4096.23 seconds wall clock time: 71 minutes 5.09 seconds (4265.09 seconds total)