Starting phenix.real_space_refine on Wed Mar 20 19:08:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/03_2024/6pkv_20367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/03_2024/6pkv_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_20367/03_2024/6pkv_20367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/03_2024/6pkv_20367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/03_2024/6pkv_20367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkv_20367/03_2024/6pkv_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-dev-5265/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: 15.82, per 1000 atoms: 0.56 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: 11.73 Conformation dependent library (CDL) restraints added in 5.8 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: 3.49 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: 11.70 Time building geometry restraints manager: 12.68 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.430 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 77.290 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.170 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.060 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 592 HIS 0.011 0.002 HIS B 259 PHE 0.025 0.002 PHE D1280 TYR 0.024 0.003 TYR B1259 ARG 0.004 0.001 ARG B 619 *********************** 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 : 3.483 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: 0.9588 (pt) cc_final: 0.9329 (mt) REVERT: A 679 LEU cc_start: 0.9209 (mp) cc_final: 0.8958 (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: 0.8702 (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: 0.3328 time to fit residues: 232.4686 Evaluate side-chains 266 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.416 ------------------------------------------------------------------------------- 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: 8.9990 chunk 174 optimal weight: 30.0000 chunk 338 optimal weight: 6.9990 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: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 707 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 HIS 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28844 Z= 0.354 Angle : 0.673 9.651 39672 Z= 0.361 Chirality : 0.040 0.155 4852 Planarity : 0.005 0.044 5124 Dihedral : 5.381 23.435 4412 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -1.00 (0.13), residues: 4060 helix: 0.40 (0.10), residues: 2584 sheet: -1.87 (0.26), residues: 352 loop : -2.67 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 592 HIS 0.010 0.001 HIS A 259 PHE 0.022 0.002 PHE A 599 TYR 0.017 0.002 TYR A 131 ARG 0.008 0.001 ARG A1092 *********************** 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 261 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 SER cc_start: 0.9180 (t) cc_final: 0.8938 (p) REVERT: A 922 PHE cc_start: 0.8478 (m-80) cc_final: 0.7961 (m-80) REVERT: B 180 TRP cc_start: 0.8424 (m-10) cc_final: 0.8139 (m-10) REVERT: B 286 SER cc_start: 0.9155 (t) cc_final: 0.8887 (p) REVERT: B 922 PHE cc_start: 0.8681 (m-80) cc_final: 0.8030 (m-80) REVERT: C 180 TRP cc_start: 0.8427 (m-10) cc_final: 0.8141 (m-10) REVERT: C 286 SER cc_start: 0.9159 (t) cc_final: 0.8891 (p) REVERT: C 922 PHE cc_start: 0.8683 (m-80) cc_final: 0.8034 (m-80) REVERT: D 180 TRP cc_start: 0.8438 (m-10) cc_final: 0.8131 (m-10) REVERT: D 286 SER cc_start: 0.9165 (t) cc_final: 0.8894 (p) REVERT: D 922 PHE cc_start: 0.8684 (m-80) cc_final: 0.8029 (m-80) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2951 time to fit residues: 136.0571 Evaluate side-chains 220 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.934 ------------------------------------------------------------------------------- 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: 20.0000 chunk 121 optimal weight: 30.0000 chunk 326 optimal weight: 0.0670 chunk 267 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 393 optimal weight: 20.0000 chunk 424 optimal weight: 50.0000 chunk 350 optimal weight: 2.9990 chunk 389 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 315 optimal weight: 5.9990 overall best weight: 7.2128 ------------------------------------------------------------------------------- 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** B 883 ASN C 883 ASN D 883 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28844 Z= 0.334 Angle : 0.641 8.366 39672 Z= 0.341 Chirality : 0.039 0.150 4852 Planarity : 0.005 0.041 5124 Dihedral : 5.031 23.736 4412 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -0.15 (0.13), residues: 4060 helix: 1.17 (0.10), residues: 2552 sheet: -1.50 (0.30), residues: 304 loop : -2.53 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP C 592 HIS 0.010 0.001 HIS A 259 PHE 0.022 0.002 PHE A 599 TYR 0.018 0.002 TYR A 131 ARG 0.003 0.001 ARG C 440 *********************** 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 243 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 SER cc_start: 0.9190 (t) cc_final: 0.8986 (p) REVERT: A 922 PHE cc_start: 0.8375 (m-80) cc_final: 0.8157 (m-80) REVERT: B 180 TRP cc_start: 0.8515 (m-10) cc_final: 0.8229 (m-10) REVERT: B 286 SER cc_start: 0.9199 (t) cc_final: 0.8983 (p) REVERT: B 922 PHE cc_start: 0.8602 (m-80) cc_final: 0.8124 (m-80) REVERT: B 1173 MET cc_start: 0.8136 (mmm) cc_final: 0.7900 (mmm) REVERT: C 180 TRP cc_start: 0.8521 (m-10) cc_final: 0.8232 (m-10) REVERT: C 286 SER cc_start: 0.9200 (t) cc_final: 0.8986 (p) REVERT: C 922 PHE cc_start: 0.8601 (m-80) cc_final: 0.8128 (m-80) REVERT: D 180 TRP cc_start: 0.8519 (m-10) cc_final: 0.8219 (m-10) REVERT: D 286 SER cc_start: 0.9209 (t) cc_final: 0.8988 (p) REVERT: D 922 PHE cc_start: 0.8594 (m-80) cc_final: 0.8116 (m-80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3140 time to fit residues: 135.2476 Evaluate side-chains 219 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.205 ------------------------------------------------------------------------------- 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: 9.9990 chunk 295 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 394 optimal weight: 50.0000 chunk 417 optimal weight: 0.0070 chunk 206 optimal weight: 50.0000 chunk 373 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2988 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= 0.164 Angle : 0.504 8.352 39672 Z= 0.264 Chirality : 0.037 0.156 4852 Planarity : 0.004 0.045 5124 Dihedral : 4.474 22.733 4412 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 0.46 (0.14), residues: 4060 helix: 1.73 (0.10), residues: 2560 sheet: -1.32 (0.30), residues: 312 loop : -2.55 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 592 HIS 0.004 0.001 HIS B 259 PHE 0.011 0.001 PHE D1280 TYR 0.013 0.001 TYR B 820 ARG 0.003 0.000 ARG A 440 *********************** 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 261 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 SER cc_start: 0.9140 (t) cc_final: 0.8886 (p) REVERT: A 922 PHE cc_start: 0.8341 (m-80) cc_final: 0.8092 (m-80) REVERT: B 180 TRP cc_start: 0.8440 (m-10) cc_final: 0.8162 (m-10) REVERT: B 286 SER cc_start: 0.9124 (t) cc_final: 0.8867 (p) REVERT: B 922 PHE cc_start: 0.8617 (m-80) cc_final: 0.8214 (m-80) REVERT: C 180 TRP cc_start: 0.8447 (m-10) cc_final: 0.8167 (m-10) REVERT: C 286 SER cc_start: 0.9127 (t) cc_final: 0.8874 (p) REVERT: C 922 PHE cc_start: 0.8626 (m-80) cc_final: 0.8221 (m-80) REVERT: D 180 TRP cc_start: 0.8451 (m-10) cc_final: 0.8164 (m-10) REVERT: D 286 SER cc_start: 0.9132 (t) cc_final: 0.8873 (p) REVERT: D 922 PHE cc_start: 0.8616 (m-80) cc_final: 0.8211 (m-80) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2990 time to fit residues: 140.0882 Evaluate side-chains 229 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 3.165 ------------------------------------------------------------------------------- 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: 0.6980 chunk 237 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 310 optimal weight: 40.0000 chunk 172 optimal weight: 20.0000 chunk 356 optimal weight: 10.0000 chunk 288 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 213 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28844 Z= 0.215 Angle : 0.530 6.670 39672 Z= 0.278 Chirality : 0.037 0.147 4852 Planarity : 0.004 0.061 5124 Dihedral : 4.372 21.880 4412 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % 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: 0.72 (0.14), residues: 4060 helix: 1.91 (0.10), residues: 2572 sheet: -0.99 (0.31), residues: 284 loop : -2.45 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 592 HIS 0.006 0.001 HIS A 259 PHE 0.013 0.001 PHE B1280 TYR 0.013 0.002 TYR C1142 ARG 0.002 0.000 ARG A 440 *********************** 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 237 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 3.203 Fit side-chains REVERT: A 286 SER cc_start: 0.9174 (t) cc_final: 0.8899 (p) REVERT: A 802 LEU cc_start: 0.9478 (tt) cc_final: 0.9213 (mm) REVERT: A 922 PHE cc_start: 0.8393 (m-80) cc_final: 0.8128 (m-80) REVERT: B 180 TRP cc_start: 0.8452 (m-10) cc_final: 0.8223 (m-10) REVERT: B 286 SER cc_start: 0.9166 (t) cc_final: 0.8886 (p) REVERT: B 922 PHE cc_start: 0.8613 (m-80) cc_final: 0.8336 (m-80) REVERT: B 1140 GLU cc_start: 0.8431 (pp20) cc_final: 0.8214 (tm-30) REVERT: C 180 TRP cc_start: 0.8455 (m-10) cc_final: 0.8227 (m-10) REVERT: C 286 SER cc_start: 0.9170 (t) cc_final: 0.8889 (p) REVERT: C 922 PHE cc_start: 0.8606 (m-80) cc_final: 0.8332 (m-80) REVERT: C 1140 GLU cc_start: 0.8435 (pp20) cc_final: 0.8214 (tm-30) REVERT: D 180 TRP cc_start: 0.8446 (m-10) cc_final: 0.8213 (m-10) REVERT: D 286 SER cc_start: 0.9165 (t) cc_final: 0.8885 (p) REVERT: D 922 PHE cc_start: 0.8597 (m-80) cc_final: 0.8330 (m-80) REVERT: D 1140 GLU cc_start: 0.8428 (pp20) cc_final: 0.8212 (tm-30) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.3057 time to fit residues: 129.2152 Evaluate side-chains 216 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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: 9.9990 chunk 82 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 219 optimal weight: 20.0000 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 538 HIS A 883 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS B 656 HIS C 538 HIS C 656 HIS D 538 HIS D 656 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28844 Z= 0.293 Angle : 0.594 7.683 39672 Z= 0.313 Chirality : 0.038 0.159 4852 Planarity : 0.004 0.047 5124 Dihedral : 4.576 22.952 4412 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % 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 (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: 0.58 (0.13), residues: 4060 helix: 1.79 (0.10), residues: 2568 sheet: -1.05 (0.31), residues: 284 loop : -2.48 (0.16), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 592 HIS 0.008 0.001 HIS A 259 PHE 0.016 0.002 PHE A 599 TYR 0.015 0.002 TYR C1142 ARG 0.004 0.000 ARG B 925 *********************** 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 237 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.480 Fit side-chains REVERT: A 802 LEU cc_start: 0.9503 (tt) cc_final: 0.9232 (mm) REVERT: B 180 TRP cc_start: 0.8480 (m-10) cc_final: 0.8254 (m-10) REVERT: B 286 SER cc_start: 0.9210 (t) cc_final: 0.8988 (p) REVERT: B 802 LEU cc_start: 0.9471 (tt) cc_final: 0.9215 (mm) REVERT: B 922 PHE cc_start: 0.8754 (m-80) cc_final: 0.8144 (m-80) REVERT: B 1140 GLU cc_start: 0.8545 (pp20) cc_final: 0.8201 (pp20) REVERT: C 180 TRP cc_start: 0.8485 (m-10) cc_final: 0.8256 (m-10) REVERT: C 286 SER cc_start: 0.9212 (t) cc_final: 0.8991 (p) REVERT: C 802 LEU cc_start: 0.9472 (tt) cc_final: 0.9218 (mm) REVERT: C 922 PHE cc_start: 0.8748 (m-80) cc_final: 0.8147 (m-80) REVERT: C 1140 GLU cc_start: 0.8549 (pp20) cc_final: 0.8202 (pp20) REVERT: D 180 TRP cc_start: 0.8477 (m-10) cc_final: 0.8241 (m-10) REVERT: D 286 SER cc_start: 0.9207 (t) cc_final: 0.8985 (p) REVERT: D 802 LEU cc_start: 0.9473 (tt) cc_final: 0.9215 (mm) REVERT: D 922 PHE cc_start: 0.8742 (m-80) cc_final: 0.8148 (m-80) REVERT: D 1140 GLU cc_start: 0.8548 (pp20) cc_final: 0.8205 (pp20) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2910 time to fit residues: 125.9170 Evaluate side-chains 210 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.158 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 305 optimal weight: 50.0000 chunk 236 optimal weight: 7.9990 chunk 351 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 416 optimal weight: 30.0000 chunk 260 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28844 Z= 0.306 Angle : 0.606 7.912 39672 Z= 0.321 Chirality : 0.039 0.189 4852 Planarity : 0.004 0.067 5124 Dihedral : 4.651 22.703 4412 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: 0.47 (0.13), residues: 4060 helix: 1.74 (0.10), residues: 2572 sheet: -1.51 (0.29), residues: 304 loop : -2.50 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 592 HIS 0.008 0.001 HIS A 259 PHE 0.015 0.002 PHE A 919 TYR 0.017 0.002 TYR D1089 ARG 0.005 0.000 ARG C 925 *********************** 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 237 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.163 Fit side-chains REVERT: A 802 LEU cc_start: 0.9507 (tt) cc_final: 0.9236 (mm) REVERT: A 922 PHE cc_start: 0.8600 (m-80) cc_final: 0.8102 (m-80) REVERT: B 180 TRP cc_start: 0.8493 (m-10) cc_final: 0.8252 (m-10) REVERT: B 802 LEU cc_start: 0.9483 (tt) cc_final: 0.9220 (mm) REVERT: B 922 PHE cc_start: 0.8780 (m-80) cc_final: 0.8159 (m-80) REVERT: B 1140 GLU cc_start: 0.8681 (pp20) cc_final: 0.8301 (pp20) REVERT: C 180 TRP cc_start: 0.8493 (m-10) cc_final: 0.8253 (m-10) REVERT: C 802 LEU cc_start: 0.9485 (tt) cc_final: 0.9226 (mm) REVERT: C 922 PHE cc_start: 0.8774 (m-80) cc_final: 0.8151 (m-80) REVERT: C 1140 GLU cc_start: 0.8688 (pp20) cc_final: 0.8303 (pp20) REVERT: D 180 TRP cc_start: 0.8487 (m-10) cc_final: 0.8248 (m-10) REVERT: D 802 LEU cc_start: 0.9485 (tt) cc_final: 0.9224 (mm) REVERT: D 922 PHE cc_start: 0.8770 (m-80) cc_final: 0.8146 (m-80) REVERT: D 1140 GLU cc_start: 0.8685 (pp20) cc_final: 0.8305 (pp20) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2917 time to fit residues: 125.3284 Evaluate side-chains 205 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.335 ------------------------------------------------------------------------------- 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: 0.9990 chunk 166 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 80 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 chunk 205 optimal weight: 40.0000 chunk 38 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.8002 moved from start: 0.4065 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= 0.233 Angle : 0.552 6.679 39672 Z= 0.289 Chirality : 0.038 0.177 4852 Planarity : 0.004 0.041 5124 Dihedral : 4.440 22.498 4412 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % 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 (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: 0.75 (0.14), residues: 4060 helix: 1.97 (0.10), residues: 2572 sheet: -1.19 (0.30), residues: 284 loop : -2.49 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 592 HIS 0.007 0.001 HIS A 259 PHE 0.012 0.001 PHE A 922 TYR 0.012 0.001 TYR D1089 ARG 0.004 0.000 ARG B 925 *********************** 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 230 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.380 Fit side-chains REVERT: A 802 LEU cc_start: 0.9500 (tt) cc_final: 0.9215 (mm) REVERT: A 922 PHE cc_start: 0.8502 (m-80) cc_final: 0.8081 (m-80) REVERT: A 1140 GLU cc_start: 0.8701 (pp20) cc_final: 0.8383 (pp20) REVERT: B 180 TRP cc_start: 0.8467 (m-10) cc_final: 0.8238 (m-10) REVERT: B 922 PHE cc_start: 0.8720 (m-80) cc_final: 0.8110 (m-80) REVERT: B 1140 GLU cc_start: 0.8776 (pp20) cc_final: 0.8426 (pp20) REVERT: C 180 TRP cc_start: 0.8485 (m-10) cc_final: 0.8239 (m-10) REVERT: C 922 PHE cc_start: 0.8745 (m-80) cc_final: 0.8127 (m-80) REVERT: C 1140 GLU cc_start: 0.8783 (pp20) cc_final: 0.8428 (pp20) REVERT: D 180 TRP cc_start: 0.8464 (m-10) cc_final: 0.8240 (m-10) REVERT: D 922 PHE cc_start: 0.8745 (m-80) cc_final: 0.8131 (m-80) REVERT: D 1140 GLU cc_start: 0.8780 (pp20) cc_final: 0.8430 (pp20) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2941 time to fit residues: 123.4140 Evaluate side-chains 207 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.464 ------------------------------------------------------------------------------- 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: 30.0000 chunk 363 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 350 optimal weight: 4.9990 chunk 366 optimal weight: 3.9990 chunk 386 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28844 Z= 0.273 Angle : 0.585 7.474 39672 Z= 0.307 Chirality : 0.038 0.178 4852 Planarity : 0.004 0.044 5124 Dihedral : 4.512 22.554 4412 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.67 (0.14), residues: 4060 helix: 1.92 (0.10), residues: 2576 sheet: -1.48 (0.28), residues: 312 loop : -2.49 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 592 HIS 0.005 0.001 HIS C 259 PHE 0.013 0.002 PHE D 665 TYR 0.016 0.002 TYR D1089 ARG 0.005 0.000 ARG C 925 *********************** 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 224 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.276 Fit side-chains REVERT: A 802 LEU cc_start: 0.9504 (tt) cc_final: 0.9219 (mm) REVERT: A 922 PHE cc_start: 0.8557 (m-80) cc_final: 0.8088 (m-80) REVERT: A 1173 MET cc_start: 0.8164 (mmm) cc_final: 0.7835 (mmt) REVERT: B 180 TRP cc_start: 0.8473 (m-10) cc_final: 0.8233 (m-10) REVERT: B 922 PHE cc_start: 0.8726 (m-80) cc_final: 0.8105 (m-80) REVERT: B 1140 GLU cc_start: 0.8767 (pp20) cc_final: 0.8335 (pp20) REVERT: C 180 TRP cc_start: 0.8486 (m-10) cc_final: 0.8242 (m-10) REVERT: C 922 PHE cc_start: 0.8722 (m-80) cc_final: 0.8103 (m-80) REVERT: C 1140 GLU cc_start: 0.8761 (pp20) cc_final: 0.8333 (pp20) REVERT: D 180 TRP cc_start: 0.8479 (m-10) cc_final: 0.8228 (m-10) REVERT: D 922 PHE cc_start: 0.8719 (m-80) cc_final: 0.8095 (m-80) REVERT: D 1140 GLU cc_start: 0.8760 (pp20) cc_final: 0.8337 (pp20) REVERT: D 1173 MET cc_start: 0.8183 (mmm) cc_final: 0.7871 (mmp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3003 time to fit residues: 122.1565 Evaluate side-chains 197 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.304 ------------------------------------------------------------------------------- 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: 2.9990 chunk 410 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 430 optimal weight: 0.0040 chunk 396 optimal weight: 6.9990 chunk 342 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 210 optimal weight: 50.0000 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1104 HIS C1104 HIS D1104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4327 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= 0.155 Angle : 0.492 6.476 39672 Z= 0.256 Chirality : 0.036 0.150 4852 Planarity : 0.003 0.040 5124 Dihedral : 4.110 21.773 4412 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.03 (0.14), residues: 4060 helix: 2.21 (0.10), residues: 2592 sheet: -1.30 (0.28), residues: 312 loop : -2.44 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 592 HIS 0.004 0.001 HIS A1161 PHE 0.010 0.001 PHE A 922 TYR 0.011 0.001 TYR D1259 ARG 0.004 0.000 ARG B 925 ********************** 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 257 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 3.000 Fit side-chains REVERT: A 922 PHE cc_start: 0.8560 (m-80) cc_final: 0.8134 (m-80) REVERT: A 1140 GLU cc_start: 0.8608 (pp20) cc_final: 0.8296 (pp20) REVERT: B 180 TRP cc_start: 0.8440 (m-10) cc_final: 0.8240 (m-10) REVERT: B 922 PHE cc_start: 0.8666 (m-80) cc_final: 0.8053 (m-80) REVERT: B 1140 GLU cc_start: 0.8610 (pp20) cc_final: 0.8339 (pp20) REVERT: C 180 TRP cc_start: 0.8444 (m-10) cc_final: 0.8243 (m-10) REVERT: C 922 PHE cc_start: 0.8696 (m-80) cc_final: 0.8077 (m-80) REVERT: C 1140 GLU cc_start: 0.8607 (pp20) cc_final: 0.8343 (pp20) REVERT: D 180 TRP cc_start: 0.8435 (m-10) cc_final: 0.8233 (m-10) REVERT: D 922 PHE cc_start: 0.8711 (m-80) cc_final: 0.8105 (m-80) REVERT: D 1140 GLU cc_start: 0.8605 (pp20) cc_final: 0.8344 (pp20) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2990 time to fit residues: 139.1064 Evaluate side-chains 221 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 3.471 ------------------------------------------------------------------------------- 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: 1.9990 chunk 365 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 316 optimal weight: 50.0000 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 343 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 352 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1057 ASN C1057 ASN D1057 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.099461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075213 restraints weight = 139458.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072642 restraints weight = 110723.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072756 restraints weight = 97798.789| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4388 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= 0.191 Angle : 0.512 6.606 39672 Z= 0.267 Chirality : 0.037 0.153 4852 Planarity : 0.004 0.038 5124 Dihedral : 4.099 22.064 4412 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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 (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: 1.13 (0.14), residues: 4060 helix: 2.26 (0.10), residues: 2596 sheet: -1.26 (0.28), residues: 312 loop : -2.38 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 592 HIS 0.004 0.001 HIS A 259 PHE 0.011 0.001 PHE A 665 TYR 0.012 0.001 TYR D1089 ARG 0.004 0.000 ARG B 925 =============================================================================== Job complete usr+sys time: 4307.21 seconds wall clock time: 78 minutes 32.28 seconds (4712.28 seconds total)