Starting phenix.real_space_refine on Sun Nov 19 23:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/11_2023/6pkv_20367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/11_2023/6pkv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/11_2023/6pkv_20367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/11_2023/6pkv_20367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/11_2023/6pkv_20367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/11_2023/6pkv_20367.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B ARG 1110": "NH1" <-> "NH2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 689": "NH1" <-> "NH2" Residue "C ARG 1110": "NH1" <-> "NH2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 689": "NH1" <-> "NH2" Residue "D ARG 1110": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 28284 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 7071 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 498} Link IDs: {'PTRANS': 35, 'TRANS': 1051} Chain breaks: 25 Unresolved non-hydrogen bonds: 1818 Unresolved non-hydrogen angles: 2295 Unresolved non-hydrogen dihedrals: 1458 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 7, 'UNK:plan-1': 22, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 4, 'ASP:plan': 33, 'PHE:plan': 18, 'GLU:plan': 64, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 1060 Chain: "B" Number of atoms: 7071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 7071 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 498} Link IDs: {'PTRANS': 35, 'TRANS': 1051} Chain breaks: 25 Unresolved non-hydrogen bonds: 1818 Unresolved non-hydrogen angles: 2295 Unresolved non-hydrogen dihedrals: 1458 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 7, 'UNK:plan-1': 22, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 4, 'ASP:plan': 33, 'PHE:plan': 18, 'GLU:plan': 64, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 1060 Chain: "C" Number of atoms: 7071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 7071 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 498} Link IDs: {'PTRANS': 35, 'TRANS': 1051} Chain breaks: 25 Unresolved non-hydrogen bonds: 1818 Unresolved non-hydrogen angles: 2295 Unresolved non-hydrogen dihedrals: 1458 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 7, 'UNK:plan-1': 22, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 4, 'ASP:plan': 33, 'PHE:plan': 18, 'GLU:plan': 64, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 1060 Chain: "D" Number of atoms: 7071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 7071 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 498} Link IDs: {'PTRANS': 35, 'TRANS': 1051} Chain breaks: 25 Unresolved non-hydrogen bonds: 1818 Unresolved non-hydrogen angles: 2295 Unresolved non-hydrogen dihedrals: 1458 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 7, 'UNK:plan-1': 22, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 4, 'ASP:plan': 33, 'PHE:plan': 18, 'GLU:plan': 64, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 1060 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: 14.98, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 11.14 Conformation dependent library (CDL) restraints added in 5.6 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: 3.72 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: 12.41 Time building geometry restraints manager: 11.96 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: 98.71 - 105.80: 507 105.80 - 112.88: 15935 112.88 - 119.97: 9266 119.97 - 127.06: 13489 127.06 - 134.14: 475 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 2.440 nonbonded pdb=" OH TYR C1283 " pdb=" OD2 ASP C1407 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR B1283 " pdb=" OD2 ASP B1407 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR A1283 " pdb=" OD2 ASP A1407 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR B 742 " pdb=" O CYS B 798 " model vdw 2.388 2.440 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.010 Extract box with map and model: 5.380 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 75.690 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.690 ------------------------------------------------------------------------------- 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= 0.334 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.970 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 outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.3353 time to fit residues: 234.2302 Evaluate side-chains 258 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 3.9990 chunk 327 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 30.0000 chunk 338 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 392 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS A1325 ASN B 193 HIS B 707 HIS ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS B1325 ASN C 193 HIS C 707 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS C1325 ASN D 193 HIS D 707 HIS ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS D1325 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 28844 Z= 0.373 Angle : 0.692 10.032 39672 Z= 0.373 Chirality : 0.040 0.159 4852 Planarity : 0.005 0.044 5124 Dihedral : 5.452 23.687 4412 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4060 helix: 0.38 (0.10), residues: 2584 sheet: -1.89 (0.26), residues: 356 loop : -2.70 (0.17), residues: 1120 *********************** 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 247 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 3.214 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3185 time to fit residues: 139.7445 Evaluate side-chains 209 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.0470 chunk 121 optimal weight: 30.0000 chunk 326 optimal weight: 0.9990 chunk 267 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 393 optimal weight: 2.9990 chunk 424 optimal weight: 40.0000 chunk 350 optimal weight: 1.9990 chunk 389 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 315 optimal weight: 9.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 HIS B 656 HIS C 656 HIS D 656 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2443 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= 0.168 Angle : 0.511 6.260 39672 Z= 0.269 Chirality : 0.037 0.137 4852 Planarity : 0.004 0.040 5124 Dihedral : 4.643 22.663 4412 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 4060 helix: 1.46 (0.10), residues: 2540 sheet: -1.48 (0.28), residues: 316 loop : -2.52 (0.17), residues: 1204 *********************** 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 266 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.354 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.3036 time to fit residues: 145.0972 Evaluate side-chains 222 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 394 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 206 optimal weight: 50.0000 chunk 373 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 883 ASN C 883 ASN D 883 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28844 Z= 0.399 Angle : 0.703 9.638 39672 Z= 0.375 Chirality : 0.041 0.177 4852 Planarity : 0.005 0.061 5124 Dihedral : 5.119 23.522 4412 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4060 helix: 1.28 (0.10), residues: 2556 sheet: -1.37 (0.30), residues: 304 loop : -2.61 (0.17), residues: 1200 *********************** 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 213 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.396 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3169 time to fit residues: 122.4129 Evaluate side-chains 195 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 213 optimal weight: 0.0050 chunk 374 optimal weight: 0.9990 chunk 105 optimal weight: 0.0010 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28844 Z= 0.138 Angle : 0.489 6.260 39672 Z= 0.254 Chirality : 0.036 0.134 4852 Planarity : 0.004 0.043 5124 Dihedral : 4.318 21.727 4412 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 4060 helix: 1.91 (0.10), residues: 2568 sheet: -1.22 (0.29), residues: 312 loop : -2.56 (0.17), residues: 1180 *********************** 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 240 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2947 time to fit residues: 129.3442 Evaluate side-chains 216 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 9.9990 chunk 376 optimal weight: 0.0270 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 103 optimal weight: 50.0000 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28844 Z= 0.225 Angle : 0.540 6.502 39672 Z= 0.282 Chirality : 0.037 0.137 4852 Planarity : 0.004 0.067 5124 Dihedral : 4.345 22.366 4412 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 4060 helix: 2.00 (0.10), residues: 2576 sheet: -1.20 (0.29), residues: 312 loop : -2.44 (0.17), residues: 1172 *********************** 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 230 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3040 time to fit residues: 127.5138 Evaluate side-chains 197 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 305 optimal weight: 50.0000 chunk 236 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 416 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 253 optimal weight: 0.0470 chunk 192 optimal weight: 1.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28844 Z= 0.174 Angle : 0.502 6.304 39672 Z= 0.260 Chirality : 0.036 0.133 4852 Planarity : 0.004 0.050 5124 Dihedral : 4.166 22.333 4412 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.05 % Allowed : 0.75 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 4060 helix: 2.16 (0.10), residues: 2564 sheet: -1.17 (0.29), residues: 312 loop : -2.40 (0.17), residues: 1184 *********************** 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 234 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 3.030 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.3031 time to fit residues: 129.3550 Evaluate side-chains 206 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 3.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 327 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 ASN B1104 HIS C1104 HIS D1104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28844 Z= 0.180 Angle : 0.502 6.281 39672 Z= 0.260 Chirality : 0.037 0.205 4852 Planarity : 0.004 0.041 5124 Dihedral : 4.087 22.428 4412 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.14), residues: 4060 helix: 2.29 (0.10), residues: 2568 sheet: -1.09 (0.29), residues: 312 loop : -2.40 (0.17), residues: 1180 *********************** 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 235 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 3.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3000 time to fit residues: 128.3018 Evaluate side-chains 212 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 30.0000 chunk 398 optimal weight: 0.8980 chunk 363 optimal weight: 0.8980 chunk 388 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 304 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 350 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28844 Z= 0.166 Angle : 0.496 6.238 39672 Z= 0.255 Chirality : 0.036 0.150 4852 Planarity : 0.004 0.039 5124 Dihedral : 3.985 22.132 4412 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 4060 helix: 2.37 (0.10), residues: 2568 sheet: -0.97 (0.29), residues: 312 loop : -2.34 (0.17), residues: 1180 *********************** 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 242 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 3.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3036 time to fit residues: 132.7248 Evaluate side-chains 215 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 0.3980 chunk 410 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 chunk 430 optimal weight: 30.0000 chunk 396 optimal weight: 20.0000 chunk 342 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 264 optimal weight: 0.7980 chunk 210 optimal weight: 50.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 28844 Z= 0.159 Angle : 0.503 11.156 39672 Z= 0.257 Chirality : 0.036 0.170 4852 Planarity : 0.004 0.036 5124 Dihedral : 3.901 22.297 4412 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 4060 helix: 2.40 (0.10), residues: 2556 sheet: -0.87 (0.29), residues: 312 loop : -2.27 (0.17), residues: 1192 ********************** 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 244 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.306 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3059 time to fit residues: 136.7023 Evaluate side-chains 219 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 343 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 352 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 HIS B 538 HIS B 669 HIS C 538 HIS C 669 HIS D 538 HIS D 669 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083089 restraints weight = 156580.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.080223 restraints weight = 128333.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080460 restraints weight = 123987.420| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28844 Z= 0.207 Angle : 0.528 9.476 39672 Z= 0.272 Chirality : 0.037 0.164 4852 Planarity : 0.004 0.034 5124 Dihedral : 4.020 22.312 4412 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 4060 helix: 2.37 (0.10), residues: 2560 sheet: -0.83 (0.29), residues: 312 loop : -2.23 (0.17), residues: 1188 =============================================================================== Job complete usr+sys time: 4333.00 seconds wall clock time: 79 minutes 54.64 seconds (4794.64 seconds total)