Starting phenix.real_space_refine on Wed Feb 21 15:23:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcq_7085/02_2024/6bcq_7085_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcq_7085/02_2024/6bcq_7085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcq_7085/02_2024/6bcq_7085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcq_7085/02_2024/6bcq_7085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcq_7085/02_2024/6bcq_7085_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcq_7085/02_2024/6bcq_7085_updated.pdb" } resolution = 3.25 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 19944 2.51 5 N 5432 2.21 5 O 5520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 949": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "B ARG 993": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1118": "NH1" <-> "NH2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "B ARG 1140": "NH1" <-> "NH2" Residue "B ARG 1146": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1063": "NH1" <-> "NH2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1140": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 380": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C ARG 571": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 878": "NH1" <-> "NH2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C ARG 953": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 1063": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "C ARG 1140": "NH1" <-> "NH2" Residue "C ARG 1146": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D ARG 380": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ARG 571": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 961": "NH1" <-> "NH2" Residue "D ARG 965": "NH1" <-> "NH2" Residue "D ARG 993": "NH1" <-> "NH2" Residue "D ARG 1063": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1137": "NH1" <-> "NH2" Residue "D ARG 1140": "NH1" <-> "NH2" Residue "D ARG 1146": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31048 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7731 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 38, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7731 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 38, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7731 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 38, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7731 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 38, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.56, per 1000 atoms: 0.50 Number of scatterers: 31048 At special positions: 0 Unit cell: (153.01, 153.01, 178.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 12 15.00 O 5520 8.00 N 5432 7.00 C 19944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.04 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.04 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.04 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.04 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: 10.38 Conformation dependent library (CDL) restraints added in 5.2 seconds 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 8 sheets defined 61.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.71 Creating SS restraints... Processing helix chain 'B' and resid 13 through 19 removed outlier: 4.173A pdb=" N LYS B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 144 through 150 Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 283 through 295 removed outlier: 4.185A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.801A pdb=" N TYR B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 391 through 403 Processing helix chain 'B' and resid 407 through 414 removed outlier: 4.116A pdb=" N SER B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.818A pdb=" N SER B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.900A pdb=" N HIS B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 464 Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 503 through 511 Processing helix chain 'B' and resid 558 through 568 Processing helix chain 'B' and resid 572 through 581 Processing helix chain 'B' and resid 585 through 601 Processing helix chain 'B' and resid 606 through 633 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 664 through 667 No H-bonds generated for 'chain 'B' and resid 664 through 667' Processing helix chain 'B' and resid 671 through 681 Processing helix chain 'B' and resid 690 through 698 Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 767 through 771 Processing helix chain 'B' and resid 775 through 798 Processing helix chain 'B' and resid 808 through 829 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 860 through 878 removed outlier: 3.814A pdb=" N LEU B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 908 removed outlier: 4.262A pdb=" N MET B 896 " --> pdb=" O CYS B 892 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B 903 " --> pdb=" O THR B 899 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL B 908 " --> pdb=" O HIS B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 947 Proline residue: B 914 - end of helix removed outlier: 4.271A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N MET B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LYS B 924 " --> pdb=" O SER B 920 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 965 through 968 No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1030 through 1066 removed outlier: 5.273A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1089 Processing helix chain 'B' and resid 1115 through 1140 Processing helix chain 'B' and resid 1143 through 1191 removed outlier: 3.676A pdb=" N GLN B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B1166 " --> pdb=" O GLY B1162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B1168 " --> pdb=" O ILE B1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS B1181 " --> pdb=" O GLU B1177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B1184 " --> pdb=" O HIS B1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 19 removed outlier: 4.172A pdb=" N LYS A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 283 through 295 removed outlier: 4.185A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.800A pdb=" N TYR A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 407 through 414 removed outlier: 4.115A pdb=" N SER A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.817A pdb=" N SER A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.899A pdb=" N HIS A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 606 through 633 Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 775 through 798 Processing helix chain 'A' and resid 808 through 829 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 860 through 878 removed outlier: 3.813A pdb=" N LEU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 908 removed outlier: 4.263A pdb=" N MET A 896 " --> pdb=" O CYS A 892 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 903 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL A 908 " --> pdb=" O HIS A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 947 Proline residue: A 914 - end of helix removed outlier: 4.271A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET A 923 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 965 through 968 No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1030 through 1066 removed outlier: 5.272A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 Processing helix chain 'A' and resid 1115 through 1140 Processing helix chain 'A' and resid 1143 through 1191 removed outlier: 3.676A pdb=" N GLN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A1168 " --> pdb=" O ILE A1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A1181 " --> pdb=" O GLU A1177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A1184 " --> pdb=" O HIS A1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 removed outlier: 4.173A pdb=" N LYS C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 133 through 142 Processing helix chain 'C' and resid 144 through 150 Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 283 through 295 removed outlier: 4.184A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 332 through 340 removed outlier: 3.801A pdb=" N TYR C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 390 through 403 Processing helix chain 'C' and resid 407 through 414 removed outlier: 4.115A pdb=" N SER C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 removed outlier: 3.817A pdb=" N SER C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 448 removed outlier: 3.900A pdb=" N HIS C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 558 through 568 Processing helix chain 'C' and resid 572 through 581 Processing helix chain 'C' and resid 585 through 601 Processing helix chain 'C' and resid 606 through 633 Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 664 through 667 No H-bonds generated for 'chain 'C' and resid 664 through 667' Processing helix chain 'C' and resid 671 through 681 Processing helix chain 'C' and resid 690 through 698 Processing helix chain 'C' and resid 700 through 702 No H-bonds generated for 'chain 'C' and resid 700 through 702' Processing helix chain 'C' and resid 767 through 771 Processing helix chain 'C' and resid 775 through 798 Processing helix chain 'C' and resid 808 through 829 Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 860 through 878 removed outlier: 3.813A pdb=" N LEU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 908 removed outlier: 4.262A pdb=" N MET C 896 " --> pdb=" O CYS C 892 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 897 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU C 903 " --> pdb=" O THR C 899 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS C 904 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL C 908 " --> pdb=" O HIS C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 947 Proline residue: C 914 - end of helix removed outlier: 4.270A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET C 922 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET C 923 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS C 924 " --> pdb=" O SER C 920 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASP C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 963 Processing helix chain 'C' and resid 965 through 968 No H-bonds generated for 'chain 'C' and resid 965 through 968' Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 1013 through 1028 Processing helix chain 'C' and resid 1030 through 1066 removed outlier: 5.272A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1089 Processing helix chain 'C' and resid 1115 through 1140 Processing helix chain 'C' and resid 1143 through 1191 removed outlier: 3.675A pdb=" N GLN C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C1164 " --> pdb=" O GLN C1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C1166 " --> pdb=" O GLY C1162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C1168 " --> pdb=" O ILE C1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C1169 " --> pdb=" O ARG C1165 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS C1181 " --> pdb=" O GLU C1177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C1184 " --> pdb=" O HIS C1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 19 removed outlier: 4.172A pdb=" N LYS D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 283 through 295 removed outlier: 4.185A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 332 through 340 removed outlier: 3.800A pdb=" N TYR D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 390 through 403 Processing helix chain 'D' and resid 407 through 414 removed outlier: 4.115A pdb=" N SER D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 3.817A pdb=" N SER D 429 " --> pdb=" O HIS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 448 removed outlier: 3.900A pdb=" N HIS D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 464 Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 558 through 568 Processing helix chain 'D' and resid 572 through 581 Processing helix chain 'D' and resid 585 through 601 Processing helix chain 'D' and resid 606 through 633 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 664 through 667 No H-bonds generated for 'chain 'D' and resid 664 through 667' Processing helix chain 'D' and resid 671 through 681 Processing helix chain 'D' and resid 690 through 698 Processing helix chain 'D' and resid 700 through 702 No H-bonds generated for 'chain 'D' and resid 700 through 702' Processing helix chain 'D' and resid 767 through 771 Processing helix chain 'D' and resid 775 through 798 Processing helix chain 'D' and resid 808 through 829 Processing helix chain 'D' and resid 849 through 856 Processing helix chain 'D' and resid 860 through 878 removed outlier: 3.813A pdb=" N LEU D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 908 removed outlier: 4.263A pdb=" N MET D 896 " --> pdb=" O CYS D 892 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 897 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU D 903 " --> pdb=" O THR D 899 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS D 904 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 907 " --> pdb=" O LEU D 903 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL D 908 " --> pdb=" O HIS D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 947 Proline residue: D 914 - end of helix removed outlier: 4.271A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET D 923 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LYS D 924 " --> pdb=" O SER D 920 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 963 Processing helix chain 'D' and resid 965 through 968 No H-bonds generated for 'chain 'D' and resid 965 through 968' Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 1013 through 1028 Processing helix chain 'D' and resid 1030 through 1066 removed outlier: 5.273A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1089 Processing helix chain 'D' and resid 1115 through 1140 Processing helix chain 'D' and resid 1143 through 1191 removed outlier: 3.676A pdb=" N GLN D1163 " --> pdb=" O LYS D1159 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D1166 " --> pdb=" O GLY D1162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D1168 " --> pdb=" O ILE D1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG D1169 " --> pdb=" O ARG D1165 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS D1181 " --> pdb=" O GLU D1177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D1184 " --> pdb=" O HIS D1180 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 21 through 24 Processing sheet with id= B, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.623A pdb=" N LEU B 92 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B 232 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE B 154 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 189 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 156 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU B 278 " --> pdb=" O PRO B 298 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 300 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 21 through 24 Processing sheet with id= D, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.623A pdb=" N LEU A 92 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 232 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE A 154 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 189 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 156 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LEU A 278 " --> pdb=" O PRO A 298 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 300 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 21 through 24 Processing sheet with id= F, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.623A pdb=" N LEU C 92 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 232 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE C 154 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 189 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 156 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU C 278 " --> pdb=" O PRO C 298 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU C 300 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 21 through 24 Processing sheet with id= H, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.623A pdb=" N LEU D 92 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 232 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE D 154 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 189 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 156 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LEU D 278 " --> pdb=" O PRO D 298 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU D 300 " --> pdb=" O LEU D 278 " (cutoff:3.500A) 1643 hydrogen bonds defined for protein. 4905 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: 11.61 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9953 1.34 - 1.46: 6167 1.46 - 1.58: 15396 1.58 - 1.69: 20 1.69 - 1.81: 208 Bond restraints: 31744 Sorted by residual: bond pdb=" C4 ATP D2000 " pdb=" C5 ATP D2000 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C4 ATP C2000 " pdb=" C5 ATP C2000 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.63e+01 bond pdb=" C5 ATP B2000 " pdb=" C6 ATP B2000 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 ... (remaining 31739 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.25: 806 106.25 - 113.67: 17902 113.67 - 121.08: 16389 121.08 - 128.50: 7683 128.50 - 135.91: 304 Bond angle restraints: 43084 Sorted by residual: angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 119.91 19.96 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PB ATP D2000 " pdb=" O3B ATP D2000 " pdb=" PG ATP D2000 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 angle pdb=" PA ATP D2000 " pdb=" O3A ATP D2000 " pdb=" PB ATP D2000 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 ... (remaining 43079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 18009 15.74 - 31.48: 651 31.48 - 47.22: 172 47.22 - 62.96: 20 62.96 - 78.71: 40 Dihedral angle restraints: 18892 sinusoidal: 7544 harmonic: 11348 Sorted by residual: dihedral pdb=" CA ILE A 279 " pdb=" C ILE A 279 " pdb=" N ASP A 280 " pdb=" CA ASP A 280 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ILE C 279 " pdb=" C ILE C 279 " pdb=" N ASP C 280 " pdb=" CA ASP C 280 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ILE D 279 " pdb=" C ILE D 279 " pdb=" N ASP D 280 " pdb=" CA ASP D 280 " ideal model delta harmonic sigma weight residual -180.00 -153.83 -26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 18889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3699 0.057 - 0.113: 1044 0.113 - 0.170: 109 0.170 - 0.226: 8 0.226 - 0.283: 16 Chirality restraints: 4876 Sorted by residual: chirality pdb=" CB VAL B1003 " pdb=" CA VAL B1003 " pdb=" CG1 VAL B1003 " pdb=" CG2 VAL B1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB VAL A1003 " pdb=" CA VAL A1003 " pdb=" CG1 VAL A1003 " pdb=" CG2 VAL A1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4873 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 700 " 0.053 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO C 701 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 701 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 701 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 700 " -0.053 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO D 701 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 701 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 701 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 700 " 0.053 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 701 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 701 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 701 " 0.044 5.00e-02 4.00e+02 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 9638 2.83 - 3.35: 28169 3.35 - 3.87: 48939 3.87 - 4.38: 55391 4.38 - 4.90: 95171 Nonbonded interactions: 237308 Sorted by model distance: nonbonded pdb=" OG1 THR C 21 " pdb=" OE2 GLU C 70 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR B 21 " pdb=" OE2 GLU B 70 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR A 21 " pdb=" OE2 GLU A 70 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR D 21 " pdb=" OE2 GLU D 70 " model vdw 2.319 2.440 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.322 2.440 ... (remaining 237303 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.360 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 75.790 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.210 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.007 0.082 31744 Z= 0.470 Angle : 1.003 19.959 43084 Z= 0.591 Chirality : 0.052 0.283 4876 Planarity : 0.007 0.078 5424 Dihedral : 10.363 78.706 11536 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.25 % Allowed : 2.37 % Favored : 97.38 % 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: -4.85 (0.09), residues: 3868 helix: -3.13 (0.06), residues: 2488 sheet: -1.66 (0.33), residues: 192 loop : -3.20 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 816 HIS 0.011 0.002 HIS A1080 PHE 0.023 0.003 PHE C 932 TYR 0.019 0.003 TYR B 228 ARG 0.012 0.001 ARG C1146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 621 time to evaluate : 3.850 Fit side-chains REVERT: B 97 ARG cc_start: 0.6469 (mtt180) cc_final: 0.5883 (ttp-170) REVERT: B 258 VAL cc_start: 0.8166 (t) cc_final: 0.7929 (m) REVERT: B 338 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6567 (mmm160) REVERT: B 353 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7743 (tp30) REVERT: B 397 GLU cc_start: 0.7231 (tt0) cc_final: 0.7002 (tt0) REVERT: B 411 GLN cc_start: 0.8174 (tt0) cc_final: 0.7944 (tp-100) REVERT: B 519 TYR cc_start: 0.3645 (t80) cc_final: 0.3318 (t80) REVERT: B 851 ARG cc_start: 0.5591 (mtt180) cc_final: 0.5035 (mmp80) REVERT: B 1089 ARG cc_start: 0.5509 (mtt180) cc_final: 0.4999 (mmm160) REVERT: B 1138 ASP cc_start: 0.7763 (m-30) cc_final: 0.7525 (m-30) REVERT: A 17 LYS cc_start: 0.6741 (mtmp) cc_final: 0.6387 (ptmt) REVERT: A 97 ARG cc_start: 0.6433 (mtt180) cc_final: 0.5915 (ttp-170) REVERT: A 258 VAL cc_start: 0.8166 (t) cc_final: 0.7936 (m) REVERT: A 338 ARG cc_start: 0.7004 (mtt180) cc_final: 0.6564 (mmm160) REVERT: A 353 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7669 (tp30) REVERT: A 397 GLU cc_start: 0.7227 (tt0) cc_final: 0.7003 (tt0) REVERT: A 411 GLN cc_start: 0.8179 (tt0) cc_final: 0.7905 (tp-100) REVERT: A 519 TYR cc_start: 0.3664 (t80) cc_final: 0.3345 (t80) REVERT: A 851 ARG cc_start: 0.5608 (mtt180) cc_final: 0.5054 (mmp80) REVERT: A 1089 ARG cc_start: 0.5562 (mtt180) cc_final: 0.5040 (mmm160) REVERT: A 1138 ASP cc_start: 0.7772 (m-30) cc_final: 0.7534 (m-30) REVERT: C 97 ARG cc_start: 0.6584 (mtt180) cc_final: 0.5975 (ttp-170) REVERT: C 258 VAL cc_start: 0.8179 (t) cc_final: 0.7961 (m) REVERT: C 338 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6801 (mmp-170) REVERT: C 353 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7747 (tp30) REVERT: C 397 GLU cc_start: 0.7204 (tt0) cc_final: 0.6986 (tt0) REVERT: C 411 GLN cc_start: 0.8179 (tt0) cc_final: 0.7946 (tp-100) REVERT: C 851 ARG cc_start: 0.5873 (mtt180) cc_final: 0.5205 (mmp80) REVERT: C 1053 TYR cc_start: 0.7437 (t80) cc_final: 0.7233 (t80) REVERT: C 1138 ASP cc_start: 0.7775 (m-30) cc_final: 0.7563 (m-30) REVERT: D 97 ARG cc_start: 0.6468 (mtt180) cc_final: 0.5885 (ttp-170) REVERT: D 258 VAL cc_start: 0.8148 (t) cc_final: 0.7923 (m) REVERT: D 338 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6576 (mmm160) REVERT: D 353 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7746 (tp30) REVERT: D 397 GLU cc_start: 0.7219 (tt0) cc_final: 0.6991 (tt0) REVERT: D 411 GLN cc_start: 0.8196 (tt0) cc_final: 0.7958 (tp-100) REVERT: D 519 TYR cc_start: 0.3582 (t80) cc_final: 0.3279 (t80) REVERT: D 851 ARG cc_start: 0.5616 (mtt180) cc_final: 0.5073 (mmp80) REVERT: D 1089 ARG cc_start: 0.5519 (mtt180) cc_final: 0.4993 (mmm160) REVERT: D 1138 ASP cc_start: 0.7768 (m-30) cc_final: 0.7538 (m-30) outliers start: 8 outliers final: 4 residues processed: 629 average time/residue: 0.5823 time to fit residues: 533.5706 Evaluate side-chains 305 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 301 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 86 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 30.0000 chunk 164 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 307 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 30.0000 chunk 228 optimal weight: 20.0000 chunk 355 optimal weight: 0.8980 overall best weight: 5.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS B 132 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 425 HIS B 570 ASN ** B 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS B1013 ASN A 88 HIS A 132 GLN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 425 HIS A 570 ASN ** A 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS A1013 ASN C 88 HIS C 132 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN C 425 HIS C 570 ASN C 782 ASN C 827 GLN ** C 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 HIS C1013 ASN D 88 HIS D 132 GLN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN D 425 HIS D 570 ASN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 HIS D1013 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31744 Z= 0.347 Angle : 0.694 9.229 43084 Z= 0.358 Chirality : 0.041 0.146 4876 Planarity : 0.006 0.066 5424 Dihedral : 7.480 82.315 4448 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.31 % Allowed : 7.12 % Favored : 90.57 % 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: -1.92 (0.12), residues: 3868 helix: -0.44 (0.10), residues: 2472 sheet: -1.56 (0.31), residues: 232 loop : -2.89 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 691 HIS 0.007 0.002 HIS C1080 PHE 0.020 0.002 PHE C 793 TYR 0.016 0.002 TYR C 855 ARG 0.009 0.001 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 310 time to evaluate : 3.828 Fit side-chains REVERT: B 97 ARG cc_start: 0.6517 (mtt180) cc_final: 0.6004 (ttp-170) REVERT: B 123 LEU cc_start: 0.6852 (mt) cc_final: 0.6029 (mm) REVERT: B 156 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 258 VAL cc_start: 0.8097 (t) cc_final: 0.7891 (m) REVERT: B 353 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7757 (tp30) REVERT: B 395 LEU cc_start: 0.7702 (tt) cc_final: 0.7499 (tp) REVERT: B 400 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8899 (mt) REVERT: B 411 GLN cc_start: 0.8231 (tt0) cc_final: 0.7988 (tp-100) REVERT: B 519 TYR cc_start: 0.3756 (t80) cc_final: 0.3442 (t80) REVERT: B 851 ARG cc_start: 0.6000 (mtt180) cc_final: 0.5345 (mmp80) REVERT: B 1138 ASP cc_start: 0.7670 (m-30) cc_final: 0.7438 (m-30) REVERT: A 97 ARG cc_start: 0.6618 (mtt180) cc_final: 0.6120 (ttp-170) REVERT: A 123 LEU cc_start: 0.6863 (mt) cc_final: 0.6065 (mm) REVERT: A 156 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8244 (p) REVERT: A 258 VAL cc_start: 0.8105 (t) cc_final: 0.7898 (m) REVERT: A 353 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7638 (tp30) REVERT: A 400 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8905 (mt) REVERT: A 411 GLN cc_start: 0.8253 (tt0) cc_final: 0.8015 (tp-100) REVERT: A 519 TYR cc_start: 0.3579 (t80) cc_final: 0.3291 (t80) REVERT: A 851 ARG cc_start: 0.6010 (mtt180) cc_final: 0.5344 (mmp80) REVERT: A 893 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9067 (tp) REVERT: A 1087 TRP cc_start: 0.5732 (t60) cc_final: 0.5387 (t60) REVERT: A 1138 ASP cc_start: 0.7678 (m-30) cc_final: 0.7442 (m-30) REVERT: C 97 ARG cc_start: 0.6521 (mtt180) cc_final: 0.6018 (ttp-170) REVERT: C 123 LEU cc_start: 0.6955 (mt) cc_final: 0.6361 (mm) REVERT: C 156 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8234 (p) REVERT: C 258 VAL cc_start: 0.8061 (t) cc_final: 0.7838 (m) REVERT: C 395 LEU cc_start: 0.7687 (tt) cc_final: 0.7484 (tp) REVERT: C 400 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8934 (mt) REVERT: C 411 GLN cc_start: 0.8244 (tt0) cc_final: 0.8009 (tp-100) REVERT: C 851 ARG cc_start: 0.6131 (mtt180) cc_final: 0.5371 (mmp80) REVERT: C 1138 ASP cc_start: 0.7779 (m-30) cc_final: 0.7570 (m-30) REVERT: D 97 ARG cc_start: 0.6517 (mtt180) cc_final: 0.6007 (ttp-170) REVERT: D 123 LEU cc_start: 0.6684 (mt) cc_final: 0.6044 (mm) REVERT: D 156 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8241 (p) REVERT: D 258 VAL cc_start: 0.8068 (t) cc_final: 0.7844 (m) REVERT: D 353 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7773 (tp30) REVERT: D 400 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8917 (mt) REVERT: D 411 GLN cc_start: 0.8230 (tt0) cc_final: 0.7984 (tp-100) REVERT: D 519 TYR cc_start: 0.3716 (t80) cc_final: 0.3424 (t80) REVERT: D 851 ARG cc_start: 0.6014 (mtt180) cc_final: 0.5347 (mmp80) REVERT: D 893 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9048 (tp) REVERT: D 1138 ASP cc_start: 0.7672 (m-30) cc_final: 0.7438 (m-30) outliers start: 75 outliers final: 40 residues processed: 382 average time/residue: 0.4891 time to fit residues: 285.0228 Evaluate side-chains 272 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 296 optimal weight: 30.0000 chunk 242 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 356 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 HIS A 88 HIS ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 HIS C 88 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 HIS D 88 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1080 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31744 Z= 0.284 Angle : 0.617 8.551 43084 Z= 0.315 Chirality : 0.039 0.153 4876 Planarity : 0.005 0.057 5424 Dihedral : 6.754 82.033 4448 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.65 % Allowed : 8.26 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3868 helix: 0.74 (0.11), residues: 2464 sheet: -1.05 (0.35), residues: 204 loop : -2.68 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 691 HIS 0.005 0.001 HIS B1080 PHE 0.019 0.002 PHE C 793 TYR 0.011 0.002 TYR C 855 ARG 0.005 0.001 ARG D1146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 250 time to evaluate : 3.932 Fit side-chains REVERT: B 97 ARG cc_start: 0.6582 (mtt180) cc_final: 0.6006 (ttp-170) REVERT: B 156 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 258 VAL cc_start: 0.8061 (t) cc_final: 0.7776 (m) REVERT: B 353 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7643 (tp30) REVERT: B 356 MET cc_start: 0.6794 (mmm) cc_final: 0.6374 (mmm) REVERT: B 395 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7500 (tp) REVERT: B 411 GLN cc_start: 0.8179 (tt0) cc_final: 0.7965 (tp-100) REVERT: B 519 TYR cc_start: 0.3712 (t80) cc_final: 0.3468 (t80) REVERT: B 851 ARG cc_start: 0.6119 (mtt180) cc_final: 0.5493 (mmp80) REVERT: A 97 ARG cc_start: 0.6667 (mtt180) cc_final: 0.6079 (ttp-110) REVERT: A 156 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8231 (p) REVERT: A 258 VAL cc_start: 0.8067 (t) cc_final: 0.7783 (m) REVERT: A 353 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7634 (tp30) REVERT: A 356 MET cc_start: 0.6809 (mmm) cc_final: 0.6411 (mmm) REVERT: A 519 TYR cc_start: 0.3742 (t80) cc_final: 0.3497 (t80) REVERT: A 691 TRP cc_start: 0.7565 (p-90) cc_final: 0.7234 (p-90) REVERT: A 851 ARG cc_start: 0.6197 (mtt180) cc_final: 0.5543 (mmp80) REVERT: A 1089 ARG cc_start: 0.5646 (mtt180) cc_final: 0.4844 (mmm160) REVERT: C 97 ARG cc_start: 0.6612 (mtt180) cc_final: 0.6042 (ttp-170) REVERT: C 156 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8217 (p) REVERT: C 258 VAL cc_start: 0.8060 (t) cc_final: 0.7780 (m) REVERT: C 356 MET cc_start: 0.6758 (mmm) cc_final: 0.6368 (mmm) REVERT: C 395 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7489 (tp) REVERT: C 411 GLN cc_start: 0.8171 (tt0) cc_final: 0.7969 (tp-100) REVERT: C 691 TRP cc_start: 0.7587 (p-90) cc_final: 0.7365 (p-90) REVERT: C 851 ARG cc_start: 0.6183 (mtt180) cc_final: 0.5513 (mmp80) REVERT: D 97 ARG cc_start: 0.6599 (mtt180) cc_final: 0.6020 (ttp-170) REVERT: D 156 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8221 (p) REVERT: D 258 VAL cc_start: 0.8065 (t) cc_final: 0.7778 (m) REVERT: D 353 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7724 (tp30) REVERT: D 356 MET cc_start: 0.6815 (mmm) cc_final: 0.6413 (mmm) REVERT: D 411 GLN cc_start: 0.8179 (tt0) cc_final: 0.7962 (tp-100) REVERT: D 519 TYR cc_start: 0.3707 (t80) cc_final: 0.3480 (t80) REVERT: D 851 ARG cc_start: 0.6149 (mtt180) cc_final: 0.5469 (mmp80) REVERT: D 1089 ARG cc_start: 0.5632 (mtt180) cc_final: 0.4798 (mmm160) outliers start: 86 outliers final: 59 residues processed: 321 average time/residue: 0.4340 time to fit residues: 221.4399 Evaluate side-chains 277 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 212 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 357 optimal weight: 2.9990 chunk 378 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 102 optimal weight: 0.0170 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 294 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31744 Z= 0.140 Angle : 0.500 7.541 43084 Z= 0.257 Chirality : 0.036 0.172 4876 Planarity : 0.004 0.060 5424 Dihedral : 6.157 78.708 4448 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.16 % Allowed : 9.74 % Favored : 88.10 % 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: 0.25 (0.14), residues: 3868 helix: 1.48 (0.11), residues: 2488 sheet: -0.95 (0.34), residues: 208 loop : -2.60 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 691 HIS 0.018 0.001 HIS B 88 PHE 0.009 0.001 PHE A 627 TYR 0.017 0.001 TYR A 339 ARG 0.007 0.000 ARG C 949 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 288 time to evaluate : 3.990 Fit side-chains REVERT: B 93 ARG cc_start: 0.4929 (tmt90) cc_final: 0.4696 (ttm170) REVERT: B 97 ARG cc_start: 0.6409 (mtt180) cc_final: 0.5888 (ttp-170) REVERT: B 258 VAL cc_start: 0.8084 (t) cc_final: 0.7800 (m) REVERT: B 353 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7731 (tp30) REVERT: B 395 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7382 (tp) REVERT: B 444 LEU cc_start: 0.9006 (tp) cc_final: 0.8780 (mm) REVERT: B 519 TYR cc_start: 0.3855 (t80) cc_final: 0.3518 (t80) REVERT: B 851 ARG cc_start: 0.6315 (mtt180) cc_final: 0.5645 (mmp80) REVERT: A 93 ARG cc_start: 0.4957 (tmt90) cc_final: 0.4729 (ttm170) REVERT: A 258 VAL cc_start: 0.8086 (t) cc_final: 0.7797 (m) REVERT: A 353 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7714 (tp30) REVERT: A 444 LEU cc_start: 0.9012 (tp) cc_final: 0.8778 (mm) REVERT: A 519 TYR cc_start: 0.3902 (t80) cc_final: 0.3564 (t80) REVERT: A 851 ARG cc_start: 0.6322 (mtt180) cc_final: 0.5650 (mmp80) REVERT: A 1089 ARG cc_start: 0.5562 (mtt180) cc_final: 0.4822 (mmm160) REVERT: C 97 ARG cc_start: 0.6531 (mtt180) cc_final: 0.5942 (ttp-170) REVERT: C 258 VAL cc_start: 0.8115 (t) cc_final: 0.7835 (m) REVERT: C 395 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7373 (tp) REVERT: C 444 LEU cc_start: 0.9007 (tp) cc_final: 0.8775 (mm) REVERT: C 851 ARG cc_start: 0.6162 (mtt180) cc_final: 0.5468 (mmp80) REVERT: D 97 ARG cc_start: 0.6406 (mtt180) cc_final: 0.5892 (ttp-170) REVERT: D 258 VAL cc_start: 0.8104 (t) cc_final: 0.7824 (m) REVERT: D 353 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7731 (tp30) REVERT: D 444 LEU cc_start: 0.9013 (tp) cc_final: 0.8780 (mm) REVERT: D 519 TYR cc_start: 0.3851 (t80) cc_final: 0.3532 (t80) REVERT: D 851 ARG cc_start: 0.6270 (mtt180) cc_final: 0.5592 (mmp80) REVERT: D 1089 ARG cc_start: 0.5485 (mtt180) cc_final: 0.4722 (mmm160) outliers start: 70 outliers final: 48 residues processed: 336 average time/residue: 0.4288 time to fit residues: 231.2078 Evaluate side-chains 281 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 193 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 90 ASN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 90 ASN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31744 Z= 0.334 Angle : 0.631 8.714 43084 Z= 0.320 Chirality : 0.041 0.167 4876 Planarity : 0.005 0.056 5424 Dihedral : 6.504 78.336 4448 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.87 % Allowed : 10.79 % Favored : 86.34 % 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: 0.19 (0.14), residues: 3868 helix: 1.44 (0.11), residues: 2472 sheet: -0.96 (0.35), residues: 208 loop : -2.61 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 691 HIS 0.005 0.001 HIS B 174 PHE 0.023 0.002 PHE C 793 TYR 0.014 0.002 TYR D 855 ARG 0.004 0.001 ARG D 637 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 233 time to evaluate : 3.936 Fit side-chains REVERT: B 93 ARG cc_start: 0.5017 (tmt90) cc_final: 0.4711 (ttm170) REVERT: B 156 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8268 (p) REVERT: B 258 VAL cc_start: 0.8162 (t) cc_final: 0.7895 (m) REVERT: B 353 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7776 (tp30) REVERT: B 356 MET cc_start: 0.6521 (mmm) cc_final: 0.6200 (mmm) REVERT: B 395 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7480 (tp) REVERT: B 691 TRP cc_start: 0.7539 (p-90) cc_final: 0.7293 (p-90) REVERT: B 851 ARG cc_start: 0.6239 (mtt180) cc_final: 0.5625 (mmp80) REVERT: B 1089 ARG cc_start: 0.5458 (mtt180) cc_final: 0.4646 (mmm160) REVERT: A 93 ARG cc_start: 0.5036 (tmt90) cc_final: 0.4770 (ttm170) REVERT: A 156 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 258 VAL cc_start: 0.8159 (t) cc_final: 0.7897 (m) REVERT: A 353 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7659 (tp30) REVERT: A 356 MET cc_start: 0.6574 (mmm) cc_final: 0.6247 (mmm) REVERT: A 519 TYR cc_start: 0.3729 (t80) cc_final: 0.3528 (t80) REVERT: A 851 ARG cc_start: 0.6177 (mtt180) cc_final: 0.5606 (mmp80) REVERT: A 1089 ARG cc_start: 0.5455 (mtt180) cc_final: 0.4630 (mmm160) REVERT: C 97 ARG cc_start: 0.6566 (mtt180) cc_final: 0.5953 (ttp-170) REVERT: C 156 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8279 (p) REVERT: C 258 VAL cc_start: 0.8140 (t) cc_final: 0.7866 (m) REVERT: C 356 MET cc_start: 0.6525 (mmm) cc_final: 0.6324 (mmt) REVERT: C 395 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7439 (tp) REVERT: C 851 ARG cc_start: 0.6118 (mtt180) cc_final: 0.5508 (mmp80) REVERT: C 1089 ARG cc_start: 0.5551 (mtt180) cc_final: 0.4708 (mmm160) REVERT: D 97 ARG cc_start: 0.6541 (mtt180) cc_final: 0.6042 (ttp-170) REVERT: D 156 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8283 (p) REVERT: D 258 VAL cc_start: 0.8192 (t) cc_final: 0.7927 (m) REVERT: D 353 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7668 (tp30) REVERT: D 691 TRP cc_start: 0.7537 (p-90) cc_final: 0.7215 (p-90) REVERT: D 851 ARG cc_start: 0.6271 (mtt180) cc_final: 0.5590 (mmp80) REVERT: D 893 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9039 (tp) REVERT: D 1089 ARG cc_start: 0.5463 (mtt180) cc_final: 0.4637 (mmm160) outliers start: 93 outliers final: 74 residues processed: 313 average time/residue: 0.4522 time to fit residues: 224.7672 Evaluate side-chains 296 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 215 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 30.0000 chunk 341 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 379 optimal weight: 0.9990 chunk 314 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 199 optimal weight: 40.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31744 Z= 0.222 Angle : 0.555 8.564 43084 Z= 0.283 Chirality : 0.038 0.167 4876 Planarity : 0.004 0.054 5424 Dihedral : 6.312 78.439 4448 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.99 % Allowed : 11.50 % Favored : 85.51 % 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: 0.51 (0.14), residues: 3868 helix: 1.72 (0.11), residues: 2476 sheet: -0.89 (0.36), residues: 208 loop : -2.56 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 691 HIS 0.005 0.001 HIS B 88 PHE 0.015 0.001 PHE A 793 TYR 0.015 0.001 TYR D 339 ARG 0.006 0.000 ARG C 949 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 235 time to evaluate : 3.568 Fit side-chains REVERT: B 93 ARG cc_start: 0.4965 (tmt90) cc_final: 0.4648 (ttm170) REVERT: B 156 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 258 VAL cc_start: 0.8194 (t) cc_final: 0.7897 (m) REVERT: B 353 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7661 (tp30) REVERT: B 356 MET cc_start: 0.6681 (mmm) cc_final: 0.6329 (mmm) REVERT: B 395 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7473 (tp) REVERT: B 444 LEU cc_start: 0.9029 (tp) cc_final: 0.8732 (mm) REVERT: B 851 ARG cc_start: 0.6300 (mtt180) cc_final: 0.5591 (mmp80) REVERT: B 1089 ARG cc_start: 0.5470 (mtt180) cc_final: 0.4633 (mmm160) REVERT: A 93 ARG cc_start: 0.5065 (tmt90) cc_final: 0.4787 (ttm170) REVERT: A 156 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8302 (p) REVERT: A 258 VAL cc_start: 0.8188 (t) cc_final: 0.7895 (m) REVERT: A 353 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7624 (tp30) REVERT: A 356 MET cc_start: 0.6691 (mmm) cc_final: 0.6324 (mmm) REVERT: A 519 TYR cc_start: 0.3848 (t80) cc_final: 0.3643 (t80) REVERT: A 851 ARG cc_start: 0.6217 (mtt180) cc_final: 0.5563 (mmp80) REVERT: A 1089 ARG cc_start: 0.5502 (mtt180) cc_final: 0.4680 (mmm160) REVERT: C 156 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8289 (p) REVERT: C 258 VAL cc_start: 0.8173 (t) cc_final: 0.7877 (m) REVERT: C 395 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7365 (tp) REVERT: C 444 LEU cc_start: 0.9026 (tp) cc_final: 0.8754 (mm) REVERT: C 851 ARG cc_start: 0.6038 (mtt180) cc_final: 0.5416 (mmp80) REVERT: C 1089 ARG cc_start: 0.5435 (mtt180) cc_final: 0.4663 (mmm160) REVERT: D 156 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8288 (p) REVERT: D 258 VAL cc_start: 0.8192 (t) cc_final: 0.7894 (m) REVERT: D 353 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7656 (tp30) REVERT: D 356 MET cc_start: 0.6676 (mmm) cc_final: 0.6322 (mmm) REVERT: D 851 ARG cc_start: 0.6323 (mtt180) cc_final: 0.5561 (mmp80) REVERT: D 1089 ARG cc_start: 0.5445 (mtt180) cc_final: 0.4612 (mmm160) outliers start: 97 outliers final: 76 residues processed: 311 average time/residue: 0.4268 time to fit residues: 213.6970 Evaluate side-chains 301 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 219 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 896 MET Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 276 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 377 optimal weight: 5.9990 chunk 236 optimal weight: 0.3980 chunk 230 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN A 88 HIS ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN D 88 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31744 Z= 0.327 Angle : 0.615 8.031 43084 Z= 0.312 Chirality : 0.041 0.174 4876 Planarity : 0.005 0.051 5424 Dihedral : 6.505 78.295 4448 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.21 % Allowed : 11.53 % Favored : 85.27 % 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 (0.14), residues: 3868 helix: 1.65 (0.11), residues: 2464 sheet: -0.89 (0.36), residues: 208 loop : -2.43 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 691 HIS 0.008 0.001 HIS D 88 PHE 0.022 0.002 PHE A 793 TYR 0.014 0.002 TYR B 339 ARG 0.006 0.001 ARG C 949 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 226 time to evaluate : 3.723 Fit side-chains revert: symmetry clash REVERT: B 93 ARG cc_start: 0.5108 (tmt90) cc_final: 0.4731 (ttm170) REVERT: B 156 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 258 VAL cc_start: 0.8169 (t) cc_final: 0.7876 (m) REVERT: B 353 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7666 (tp30) REVERT: B 395 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7465 (tp) REVERT: B 851 ARG cc_start: 0.6177 (mtt180) cc_final: 0.5409 (mmp80) REVERT: B 1089 ARG cc_start: 0.5498 (mtt180) cc_final: 0.4560 (mmm160) REVERT: A 93 ARG cc_start: 0.5106 (tmt90) cc_final: 0.4771 (ttm170) REVERT: A 156 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 258 VAL cc_start: 0.8162 (t) cc_final: 0.7875 (m) REVERT: A 353 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7669 (tp30) REVERT: A 356 MET cc_start: 0.6723 (mmm) cc_final: 0.6386 (mmm) REVERT: A 519 TYR cc_start: 0.3867 (t80) cc_final: 0.3659 (t80) REVERT: A 691 TRP cc_start: 0.7557 (p-90) cc_final: 0.7285 (p-90) REVERT: A 851 ARG cc_start: 0.6181 (mtt180) cc_final: 0.5412 (mmp80) REVERT: A 1089 ARG cc_start: 0.5564 (mtt180) cc_final: 0.4738 (mmm160) REVERT: C 156 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8320 (p) REVERT: C 258 VAL cc_start: 0.8150 (t) cc_final: 0.7879 (m) REVERT: C 395 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7442 (tp) REVERT: C 691 TRP cc_start: 0.7533 (p-90) cc_final: 0.7238 (p-90) REVERT: C 851 ARG cc_start: 0.6092 (mtt180) cc_final: 0.5359 (mmp80) REVERT: C 1089 ARG cc_start: 0.5454 (mtt180) cc_final: 0.4663 (mmm160) REVERT: D 156 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8291 (p) REVERT: D 258 VAL cc_start: 0.8163 (t) cc_final: 0.7868 (m) REVERT: D 353 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7663 (tp30) REVERT: D 851 ARG cc_start: 0.6054 (mtt180) cc_final: 0.5354 (mmp80) REVERT: D 1089 ARG cc_start: 0.5481 (mtt180) cc_final: 0.4543 (mmm160) outliers start: 104 outliers final: 89 residues processed: 314 average time/residue: 0.4947 time to fit residues: 253.0036 Evaluate side-chains 311 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 216 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 186 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 296 optimal weight: 40.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS B 160 HIS A 88 HIS A 160 HIS ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 160 HIS ** C1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 160 HIS ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31744 Z= 0.155 Angle : 0.506 7.992 43084 Z= 0.260 Chirality : 0.037 0.166 4876 Planarity : 0.004 0.050 5424 Dihedral : 6.082 78.405 4448 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.02 % Allowed : 11.99 % Favored : 84.99 % 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: 0.92 (0.14), residues: 3868 helix: 2.02 (0.11), residues: 2484 sheet: -0.77 (0.36), residues: 208 loop : -2.38 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 691 HIS 0.011 0.001 HIS C 88 PHE 0.016 0.001 PHE A 91 TYR 0.018 0.001 TYR D 339 ARG 0.007 0.000 ARG C 949 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 257 time to evaluate : 3.419 Fit side-chains REVERT: B 87 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7414 (ptmm) REVERT: B 93 ARG cc_start: 0.5159 (tmt90) cc_final: 0.4922 (ttm170) REVERT: B 156 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 258 VAL cc_start: 0.8150 (t) cc_final: 0.7852 (m) REVERT: B 353 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7640 (tp30) REVERT: B 395 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7310 (tp) REVERT: B 400 LEU cc_start: 0.9113 (mt) cc_final: 0.8894 (mt) REVERT: B 444 LEU cc_start: 0.9020 (tp) cc_final: 0.8721 (mm) REVERT: B 851 ARG cc_start: 0.6070 (mtt180) cc_final: 0.5370 (mmp80) REVERT: B 1089 ARG cc_start: 0.5439 (mtt180) cc_final: 0.4619 (mmm160) REVERT: A 87 LYS cc_start: 0.7794 (mmmm) cc_final: 0.7425 (ptmm) REVERT: A 156 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8296 (p) REVERT: A 258 VAL cc_start: 0.8148 (t) cc_final: 0.7853 (m) REVERT: A 353 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7546 (tp30) REVERT: A 356 MET cc_start: 0.6591 (mmm) cc_final: 0.6221 (mmm) REVERT: A 519 TYR cc_start: 0.3874 (t80) cc_final: 0.3669 (t80) REVERT: A 851 ARG cc_start: 0.6075 (mtt180) cc_final: 0.5371 (mmp80) REVERT: A 1089 ARG cc_start: 0.5445 (mtt180) cc_final: 0.4661 (mmm160) REVERT: C 87 LYS cc_start: 0.7747 (mmmm) cc_final: 0.7364 (ptmm) REVERT: C 156 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8309 (p) REVERT: C 258 VAL cc_start: 0.8149 (t) cc_final: 0.7849 (m) REVERT: C 395 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7275 (tp) REVERT: C 444 LEU cc_start: 0.9020 (tp) cc_final: 0.8746 (mm) REVERT: C 691 TRP cc_start: 0.7503 (p-90) cc_final: 0.7288 (p-90) REVERT: C 851 ARG cc_start: 0.5925 (mtt180) cc_final: 0.5191 (mmp80) REVERT: C 1089 ARG cc_start: 0.5471 (mtt180) cc_final: 0.4729 (mmm160) REVERT: D 87 LYS cc_start: 0.7712 (mmmm) cc_final: 0.7352 (ptmm) REVERT: D 156 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8285 (p) REVERT: D 258 VAL cc_start: 0.8175 (t) cc_final: 0.7879 (m) REVERT: D 353 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7643 (tp30) REVERT: D 851 ARG cc_start: 0.6132 (mtt180) cc_final: 0.5376 (mmp80) REVERT: D 1089 ARG cc_start: 0.5457 (mtt180) cc_final: 0.4537 (mmm160) outliers start: 98 outliers final: 73 residues processed: 335 average time/residue: 0.4272 time to fit residues: 230.3399 Evaluate side-chains 307 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 228 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 352 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 318 optimal weight: 7.9990 chunk 332 optimal weight: 6.9990 chunk 350 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS A 88 HIS C 88 HIS C 827 GLN D 88 HIS D 90 ASN D 349 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31744 Z= 0.271 Angle : 0.576 8.905 43084 Z= 0.291 Chirality : 0.040 0.161 4876 Planarity : 0.004 0.052 5424 Dihedral : 6.245 77.543 4448 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.71 % Allowed : 12.36 % Favored : 84.93 % 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: 0.85 (0.14), residues: 3868 helix: 1.97 (0.11), residues: 2468 sheet: -0.74 (0.36), residues: 208 loop : -2.35 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 691 HIS 0.007 0.001 HIS D 88 PHE 0.017 0.002 PHE D 793 TYR 0.019 0.002 TYR A 814 ARG 0.007 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 223 time to evaluate : 3.738 Fit side-chains REVERT: B 87 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7438 (ptmm) REVERT: B 93 ARG cc_start: 0.5347 (tmt90) cc_final: 0.5085 (ttm170) REVERT: B 156 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 258 VAL cc_start: 0.8180 (t) cc_final: 0.7881 (m) REVERT: B 353 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7666 (tp30) REVERT: B 395 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7400 (tp) REVERT: B 691 TRP cc_start: 0.7526 (p-90) cc_final: 0.7177 (p-90) REVERT: B 851 ARG cc_start: 0.6112 (mtt180) cc_final: 0.5387 (mmp80) REVERT: B 1089 ARG cc_start: 0.5529 (mtt180) cc_final: 0.4606 (mmm160) REVERT: A 87 LYS cc_start: 0.7850 (mmmm) cc_final: 0.7448 (ptmm) REVERT: A 156 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8308 (p) REVERT: A 258 VAL cc_start: 0.8181 (t) cc_final: 0.7898 (m) REVERT: A 353 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7630 (tp30) REVERT: A 356 MET cc_start: 0.6620 (mmm) cc_final: 0.6263 (mmm) REVERT: A 851 ARG cc_start: 0.6114 (mtt180) cc_final: 0.5391 (mmp80) REVERT: A 1089 ARG cc_start: 0.5588 (mtt180) cc_final: 0.4602 (mmm160) REVERT: C 87 LYS cc_start: 0.7768 (mmmm) cc_final: 0.7300 (ptmm) REVERT: C 156 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8283 (p) REVERT: C 258 VAL cc_start: 0.8183 (t) cc_final: 0.7896 (m) REVERT: C 395 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7282 (tp) REVERT: C 851 ARG cc_start: 0.5976 (mtt180) cc_final: 0.5248 (mmp80) REVERT: C 1089 ARG cc_start: 0.5524 (mtt180) cc_final: 0.4802 (mmm160) REVERT: D 87 LYS cc_start: 0.7783 (mmmm) cc_final: 0.7455 (ptmm) REVERT: D 156 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8303 (p) REVERT: D 258 VAL cc_start: 0.8201 (t) cc_final: 0.7909 (m) REVERT: D 353 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7670 (tp30) REVERT: D 691 TRP cc_start: 0.7527 (p-90) cc_final: 0.7178 (p-90) REVERT: D 851 ARG cc_start: 0.6122 (mtt180) cc_final: 0.5391 (mmp80) REVERT: D 1089 ARG cc_start: 0.5513 (mtt180) cc_final: 0.4593 (mmm160) outliers start: 88 outliers final: 78 residues processed: 297 average time/residue: 0.4287 time to fit residues: 205.5746 Evaluate side-chains 301 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 217 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.7980 chunk 372 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 390 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 310 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS A 88 HIS A 349 GLN C 88 HIS D 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31744 Z= 0.192 Angle : 0.533 9.496 43084 Z= 0.270 Chirality : 0.038 0.163 4876 Planarity : 0.004 0.052 5424 Dihedral : 6.116 77.702 4448 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.65 % Allowed : 12.48 % Favored : 84.86 % 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: 1.01 (0.14), residues: 3868 helix: 2.09 (0.11), residues: 2476 sheet: -0.67 (0.36), residues: 208 loop : -2.30 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 691 HIS 0.006 0.001 HIS C 88 PHE 0.012 0.001 PHE D 91 TYR 0.018 0.001 TYR D 339 ARG 0.008 0.000 ARG C 949 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 236 time to evaluate : 3.737 Fit side-chains REVERT: B 87 LYS cc_start: 0.7706 (mmmm) cc_final: 0.7274 (ptmm) REVERT: B 93 ARG cc_start: 0.5263 (tmt90) cc_final: 0.4999 (ttm170) REVERT: B 156 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8323 (p) REVERT: B 258 VAL cc_start: 0.8156 (t) cc_final: 0.7854 (m) REVERT: B 353 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7627 (tp30) REVERT: B 395 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7334 (tp) REVERT: B 691 TRP cc_start: 0.7473 (p-90) cc_final: 0.7212 (p-90) REVERT: B 851 ARG cc_start: 0.6122 (mtt180) cc_final: 0.5380 (mmp80) REVERT: B 1089 ARG cc_start: 0.5511 (mtt180) cc_final: 0.4599 (mmm160) REVERT: A 87 LYS cc_start: 0.7711 (mmmm) cc_final: 0.7379 (ptmm) REVERT: A 156 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 258 VAL cc_start: 0.8157 (t) cc_final: 0.7862 (m) REVERT: A 353 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7649 (tp30) REVERT: A 356 MET cc_start: 0.6569 (mmm) cc_final: 0.6212 (mmm) REVERT: A 851 ARG cc_start: 0.6132 (mtt180) cc_final: 0.5384 (mmp80) REVERT: A 1089 ARG cc_start: 0.5570 (mtt180) cc_final: 0.4591 (mmm160) REVERT: C 87 LYS cc_start: 0.7677 (mmmm) cc_final: 0.7279 (ptmm) REVERT: C 156 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8320 (p) REVERT: C 258 VAL cc_start: 0.8186 (t) cc_final: 0.7887 (m) REVERT: C 395 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7280 (tp) REVERT: C 444 LEU cc_start: 0.9031 (tp) cc_final: 0.8744 (mm) REVERT: C 851 ARG cc_start: 0.6063 (mtt180) cc_final: 0.5238 (mmp80) REVERT: C 1089 ARG cc_start: 0.5512 (mtt180) cc_final: 0.4796 (mmm160) REVERT: D 87 LYS cc_start: 0.7754 (mmmm) cc_final: 0.7330 (ptmm) REVERT: D 156 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8316 (p) REVERT: D 258 VAL cc_start: 0.8181 (t) cc_final: 0.7882 (m) REVERT: D 353 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7624 (tp30) REVERT: D 691 TRP cc_start: 0.7475 (p-90) cc_final: 0.7214 (p-90) REVERT: D 851 ARG cc_start: 0.6156 (mtt180) cc_final: 0.5394 (mmp80) REVERT: D 1089 ARG cc_start: 0.5524 (mtt180) cc_final: 0.4532 (mmm160) outliers start: 86 outliers final: 78 residues processed: 304 average time/residue: 0.4316 time to fit residues: 210.6903 Evaluate side-chains 313 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 229 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 670 ASP Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 670 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 311 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 319 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS A 88 HIS C 88 HIS C 90 ASN D 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.126087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093509 restraints weight = 73826.743| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.42 r_work: 0.3288 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31744 Z= 0.227 Angle : 0.557 11.043 43084 Z= 0.279 Chirality : 0.039 0.161 4876 Planarity : 0.004 0.051 5424 Dihedral : 6.143 77.420 4448 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.71 % Allowed : 12.30 % Favored : 84.99 % 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: 1.01 (0.14), residues: 3868 helix: 2.08 (0.11), residues: 2472 sheet: -0.63 (0.36), residues: 208 loop : -2.29 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 691 HIS 0.006 0.001 HIS D 88 PHE 0.014 0.001 PHE B 793 TYR 0.019 0.001 TYR D 814 ARG 0.008 0.000 ARG C 949 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.37 seconds wall clock time: 118 minutes 14.09 seconds (7094.09 seconds total)