Starting phenix.real_space_refine on Fri Mar 6 15:59:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddq_27338/03_2026/8ddq_27338.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddq_27338/03_2026/8ddq_27338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ddq_27338/03_2026/8ddq_27338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddq_27338/03_2026/8ddq_27338.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddq_27338/03_2026/8ddq_27338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddq_27338/03_2026/8ddq_27338.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 232 5.16 5 Na 2 4.78 5 C 20672 2.51 5 N 5344 2.21 5 O 5588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7798 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7961 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7798 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7961 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7798 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7961 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 7798 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 962, 7790 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 38, 'TRANS': 923} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7961 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {' NA': 2, '3PH': 1, '9Z9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'3PH': 1, '9Z9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'3PH': 1, '9Z9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'3PH': 1, '9Z9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AMET A1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET A1011 " occ=0.43 residue: pdb=" N AMET B1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET B1011 " occ=0.43 residue: pdb=" N AMET C1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET C1011 " occ=0.43 residue: pdb=" N AMET D1011 " occ=0.57 ... (14 atoms not shown) pdb=" CE BMET D1011 " occ=0.43 Time building chain proxies: 12.65, per 1000 atoms: 0.40 Number of scatterers: 31842 At special positions: 0 Unit cell: (145.34, 146.2, 158.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 232 16.00 P 4 15.00 Na 2 11.00 O 5588 8.00 N 5344 7.00 C 20672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 2.4 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 7 sheets defined 67.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 201 through 216 removed outlier: 4.233A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.816A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.849A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 342 through 354 removed outlier: 4.075A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.619A pdb=" N ILE A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.730A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 476 removed outlier: 3.674A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.686A pdb=" N GLN A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 removed outlier: 3.570A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.623A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.842A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.809A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 689 through 717 removed outlier: 3.868A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 729 through 733 removed outlier: 4.038A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 784 through 790 removed outlier: 3.740A pdb=" N LEU A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 870 through 895 Processing helix chain 'A' and resid 902 through 922 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.539A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.748A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 removed outlier: 4.202A pdb=" N ILE A 980 " --> pdb=" O CYS A 976 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 3.789A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1033 removed outlier: 3.701A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1013 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A1015 " --> pdb=" O AMET A1011 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1046 removed outlier: 3.772A pdb=" N LYS A1044 " --> pdb=" O TRP A1040 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1054 removed outlier: 3.854A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1064 Processing helix chain 'A' and resid 1089 through 1104 removed outlier: 4.267A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1117 removed outlier: 3.626A pdb=" N ASN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1142 removed outlier: 3.509A pdb=" N VAL A1121 " --> pdb=" O THR A1117 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A1136 " --> pdb=" O GLN A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1158 removed outlier: 4.055A pdb=" N MET A1156 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.676A pdb=" N ARG A1240 " --> pdb=" O GLU A1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.876A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.559A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 342 through 354 removed outlier: 4.109A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.593A pdb=" N ILE B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.093A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.730A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 476 removed outlier: 3.698A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.653A pdb=" N GLN B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 536 through 545 removed outlier: 3.570A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.629A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.792A pdb=" N ASN B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 removed outlier: 3.841A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.809A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 684 Processing helix chain 'B' and resid 689 through 717 removed outlier: 4.243A pdb=" N GLN B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.898A pdb=" N SER B 733 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 784 through 790 removed outlier: 3.733A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 868 Processing helix chain 'B' and resid 870 through 895 Processing helix chain 'B' and resid 902 through 924 Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.668A pdb=" N VAL B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 962 removed outlier: 3.520A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.200A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.781A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1033 removed outlier: 3.728A pdb=" N TYR B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B1015 " --> pdb=" O AMET B1011 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1046 removed outlier: 3.739A pdb=" N LYS B1044 " --> pdb=" O TRP B1040 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1054 removed outlier: 3.896A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1064 Processing helix chain 'B' and resid 1089 through 1104 removed outlier: 4.263A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1117 removed outlier: 3.602A pdb=" N ASN B1108 " --> pdb=" O ILE B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1117 through 1142 removed outlier: 3.519A pdb=" N VAL B1121 " --> pdb=" O THR B1117 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B1136 " --> pdb=" O GLN B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1158 removed outlier: 3.923A pdb=" N MET B1156 " --> pdb=" O ILE B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.692A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 5 removed outlier: 4.023A pdb=" N UNK F 5 " --> pdb=" O UNK F 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 201 through 216 removed outlier: 4.284A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 244 removed outlier: 3.702A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 342 through 354 removed outlier: 4.088A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.550A pdb=" N ILE C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.127A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.664A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 476 removed outlier: 3.680A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 499 removed outlier: 3.589A pdb=" N GLN C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 removed outlier: 3.590A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.559A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.860A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 3.838A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.790A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 690 through 717 removed outlier: 4.013A pdb=" N GLU C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 Processing helix chain 'C' and resid 729 through 733 removed outlier: 3.912A pdb=" N SER C 733 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 783 Processing helix chain 'C' and resid 784 through 790 removed outlier: 3.700A pdb=" N LEU C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 868 Processing helix chain 'C' and resid 870 through 895 Processing helix chain 'C' and resid 902 through 924 removed outlier: 3.512A pdb=" N ILE C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 924 " --> pdb=" O MET C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 939 removed outlier: 3.644A pdb=" N VAL C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.536A pdb=" N LEU C 962 " --> pdb=" O MET C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 removed outlier: 4.207A pdb=" N ILE C 980 " --> pdb=" O CYS C 976 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR C 981 " --> pdb=" O VAL C 977 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 3.781A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1033 removed outlier: 3.716A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP C1009 " --> pdb=" O LYS C1005 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C1013 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1046 removed outlier: 3.725A pdb=" N LYS C1044 " --> pdb=" O TRP C1040 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1054 removed outlier: 3.903A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1064 Processing helix chain 'C' and resid 1089 through 1104 removed outlier: 4.267A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1116 removed outlier: 3.625A pdb=" N ASN C1108 " --> pdb=" O ILE C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1117 through 1142 removed outlier: 4.651A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C1136 " --> pdb=" O GLN C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1158 removed outlier: 3.887A pdb=" N MET C1156 " --> pdb=" O ILE C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1214 Processing helix chain 'C' and resid 1215 through 1240 removed outlier: 3.707A pdb=" N ARG C1240 " --> pdb=" O GLU C1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 201 through 216 removed outlier: 4.172A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 244 removed outlier: 3.751A pdb=" N SER D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.863A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 378 removed outlier: 3.597A pdb=" N ILE D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.803A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 450 removed outlier: 3.690A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 476 removed outlier: 3.696A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 499 removed outlier: 3.658A pdb=" N GLN D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 removed outlier: 3.621A pdb=" N LEU D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.615A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 577 Processing helix chain 'D' and resid 578 through 587 removed outlier: 3.856A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.837A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.786A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 Processing helix chain 'D' and resid 689 through 717 removed outlier: 3.870A pdb=" N GLN D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 Processing helix chain 'D' and resid 752 through 765 Processing helix chain 'D' and resid 774 through 783 Processing helix chain 'D' and resid 784 through 790 removed outlier: 3.773A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 868 Processing helix chain 'D' and resid 870 through 895 Processing helix chain 'D' and resid 902 through 924 removed outlier: 3.508A pdb=" N LEU D 924 " --> pdb=" O MET D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 939 removed outlier: 3.648A pdb=" N VAL D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 962 removed outlier: 3.709A pdb=" N LEU D 962 " --> pdb=" O MET D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.201A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.788A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1033 removed outlier: 3.717A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D1015 " --> pdb=" O AMET D1011 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1046 removed outlier: 3.757A pdb=" N LYS D1044 " --> pdb=" O TRP D1040 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1054 removed outlier: 3.890A pdb=" N ILE D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1064 Processing helix chain 'D' and resid 1089 through 1104 removed outlier: 4.286A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1117 removed outlier: 3.622A pdb=" N ASN D1108 " --> pdb=" O ILE D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1142 removed outlier: 3.510A pdb=" N VAL D1121 " --> pdb=" O THR D1117 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D1136 " --> pdb=" O GLN D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1150 Processing helix chain 'D' and resid 1151 through 1158 Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 3.713A pdb=" N ARG D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 275 removed outlier: 6.564A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA A 218 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE A 251 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 184 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE A 221 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL A 362 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA A 336 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS A 364 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE A 338 " --> pdb=" O CYS A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 275 removed outlier: 6.578A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA B 218 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 251 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 220 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 253 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 184 " --> pdb=" O TRP B 219 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE B 221 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N CYS B 364 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 338 " --> pdb=" O CYS B 364 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 361 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE B 430 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 363 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 137 removed outlier: 3.754A pdb=" N UNK G 10 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 275 removed outlier: 6.556A pdb=" N THR C 250 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE C 295 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY C 252 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA C 297 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA C 254 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA C 218 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 184 " --> pdb=" O TRP C 219 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE C 221 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 186 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N VAL C 362 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA C 336 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N CYS C 364 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE C 338 " --> pdb=" O CYS C 364 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 361 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE C 430 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 363 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 271 through 275 removed outlier: 6.583A pdb=" N THR D 250 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE D 295 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA D 218 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE D 251 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU D 184 " --> pdb=" O TRP D 219 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE D 221 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE D 186 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N VAL D 362 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 336 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N CYS D 364 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE D 338 " --> pdb=" O CYS D 364 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 361 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE D 430 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL D 363 " --> pdb=" O PHE D 430 " (cutoff:3.500A) 1741 hydrogen bonds defined for protein. 5149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 16 1.04 - 1.26: 5032 1.26 - 1.47: 12729 1.47 - 1.68: 14367 1.68 - 1.90: 432 Bond restraints: 32576 Sorted by residual: bond pdb=" C03 9Z9 C1401 " pdb=" C74 9Z9 C1401 " ideal model delta sigma weight residual 1.534 0.828 0.706 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C03 9Z9 D1401 " pdb=" C74 9Z9 D1401 " ideal model delta sigma weight residual 1.534 0.829 0.705 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C03 9Z9 A1402 " pdb=" C74 9Z9 A1402 " ideal model delta sigma weight residual 1.534 0.829 0.705 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C03 9Z9 B1401 " pdb=" C74 9Z9 B1401 " ideal model delta sigma weight residual 1.534 0.830 0.704 2.00e-02 2.50e+03 1.24e+03 bond pdb=" C02 9Z9 B1401 " pdb=" C03 9Z9 B1401 " ideal model delta sigma weight residual 1.544 1.005 0.539 2.00e-02 2.50e+03 7.27e+02 ... (remaining 32571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.63: 44036 10.63 - 21.26: 8 21.26 - 31.89: 8 31.89 - 42.52: 4 42.52 - 53.15: 4 Bond angle restraints: 44060 Sorted by residual: angle pdb=" C74 9Z9 B1401 " pdb=" C73 9Z9 B1401 " pdb=" C76 9Z9 B1401 " ideal model delta sigma weight residual 114.05 167.20 -53.15 3.00e+00 1.11e-01 3.14e+02 angle pdb=" C74 9Z9 D1401 " pdb=" C73 9Z9 D1401 " pdb=" C76 9Z9 D1401 " ideal model delta sigma weight residual 114.05 167.19 -53.14 3.00e+00 1.11e-01 3.14e+02 angle pdb=" C74 9Z9 C1401 " pdb=" C73 9Z9 C1401 " pdb=" C76 9Z9 C1401 " ideal model delta sigma weight residual 114.05 167.15 -53.10 3.00e+00 1.11e-01 3.13e+02 angle pdb=" C74 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" C76 9Z9 A1402 " ideal model delta sigma weight residual 114.05 167.13 -53.08 3.00e+00 1.11e-01 3.13e+02 angle pdb=" C76 9Z9 D1401 " pdb=" C73 9Z9 D1401 " pdb=" O72 9Z9 D1401 " ideal model delta sigma weight residual 109.02 71.70 37.32 3.00e+00 1.11e-01 1.55e+02 ... (remaining 44055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.16: 19254 27.16 - 54.32: 523 54.32 - 81.47: 58 81.47 - 108.63: 0 108.63 - 135.79: 4 Dihedral angle restraints: 19839 sinusoidal: 8403 harmonic: 11436 Sorted by residual: dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA THR B 356 " pdb=" C THR B 356 " pdb=" N PRO B 357 " pdb=" CA PRO B 357 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 19836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.376: 4908 0.376 - 0.751: 8 0.751 - 1.127: 4 1.127 - 1.503: 0 1.503 - 1.878: 4 Chirality restraints: 4924 Sorted by residual: chirality pdb=" C03 9Z9 C1401 " pdb=" C02 9Z9 C1401 " pdb=" C04 9Z9 C1401 " pdb=" C74 9Z9 C1401 " both_signs ideal model delta sigma weight residual False 2.78 0.90 1.88 2.00e-01 2.50e+01 8.82e+01 chirality pdb=" C03 9Z9 D1401 " pdb=" C02 9Z9 D1401 " pdb=" C04 9Z9 D1401 " pdb=" C74 9Z9 D1401 " both_signs ideal model delta sigma weight residual False 2.78 0.90 1.88 2.00e-01 2.50e+01 8.82e+01 chirality pdb=" C03 9Z9 B1401 " pdb=" C02 9Z9 B1401 " pdb=" C04 9Z9 B1401 " pdb=" C74 9Z9 B1401 " both_signs ideal model delta sigma weight residual False 2.78 0.90 1.88 2.00e-01 2.50e+01 8.82e+01 ... (remaining 4921 not shown) Planarity restraints: 5480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1146 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A1147 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A1147 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1147 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C1146 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO C1147 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C1147 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C1147 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1146 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO D1147 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D1147 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D1147 " 0.026 5.00e-02 4.00e+02 ... (remaining 5477 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5245 2.76 - 3.30: 30589 3.30 - 3.83: 50884 3.83 - 4.37: 59504 4.37 - 4.90: 105131 Nonbonded interactions: 251353 Sorted by model distance: nonbonded pdb=" NH1 ARG A 369 " pdb=" OH TYR A 405 " model vdw 2.231 3.120 nonbonded pdb=" C01 9Z9 A1402 " pdb=" C74 9Z9 A1402 " model vdw 2.249 2.944 nonbonded pdb=" C01 9Z9 B1401 " pdb=" C74 9Z9 B1401 " model vdw 2.249 2.944 nonbonded pdb=" C01 9Z9 C1401 " pdb=" C74 9Z9 C1401 " model vdw 2.250 2.944 nonbonded pdb=" C01 9Z9 D1401 " pdb=" C74 9Z9 D1401 " model vdw 2.250 2.944 ... (remaining 251348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 129 through 1010 or resid 1012 through 1243)) selection = (chain 'B' and (resid 129 through 1010 or resid 1012 through 1243)) selection = (chain 'C' and (resid 129 through 1010 or resid 1012 through 1243)) selection = (chain 'D' and (resid 129 through 1010 or resid 1012 through 1243)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 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: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.140 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.015 0.706 32576 Z= 0.747 Angle : 0.962 53.150 44060 Z= 0.379 Chirality : 0.074 1.878 4924 Planarity : 0.004 0.061 5480 Dihedral : 12.332 135.790 12447 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.61 % Allowed : 5.30 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.14), residues: 3812 helix: 1.61 (0.11), residues: 2416 sheet: 0.02 (0.32), residues: 220 loop : -1.34 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.014 0.001 TYR C1048 PHE 0.009 0.001 PHE C 913 TRP 0.012 0.001 TRP A 763 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.01500 (32576) covalent geometry : angle 0.96191 (44060) hydrogen bonds : bond 0.15212 ( 1741) hydrogen bonds : angle 4.80973 ( 5149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 506 time to evaluate : 1.268 Fit side-chains REVERT: B 633 HIS cc_start: 0.6492 (OUTLIER) cc_final: 0.5605 (t-90) REVERT: B 1064 ASP cc_start: 0.6530 (t70) cc_final: 0.6294 (t0) REVERT: B 1156 MET cc_start: 0.2917 (mpp) cc_final: 0.2679 (mpm) REVERT: C 413 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5422 (mt) REVERT: D 172 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8189 (tp) REVERT: D 1115 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8298 (m-40) outliers start: 55 outliers final: 16 residues processed: 551 average time/residue: 0.7716 time to fit residues: 495.7016 Evaluate side-chains 403 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 383 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 1115 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 198 GLN A 288 ASN A 531 HIS A 632 ASN A 697 HIS A 739 GLN A 933 GLN A 963 GLN A1116 ASN A1199 GLN A1229 ASN B 134 GLN B 193 GLN B 198 GLN B 240 HIS B 437 HIS B 531 HIS B 632 ASN B 697 HIS B 739 GLN B 933 GLN B1116 ASN B1199 GLN B1229 ASN C 134 GLN C 288 ASN C 409 GLN C 412 HIS C 632 ASN C 685 ASN C 697 HIS C 739 GLN C 933 GLN C1116 ASN C1199 GLN C1229 ASN D 134 GLN D 194 ASN D 198 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS D 539 HIS D 632 ASN D 697 HIS D 739 GLN D 963 GLN D1116 ASN D1199 GLN D1229 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119968 restraints weight = 76141.893| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.77 r_work: 0.3293 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32576 Z= 0.147 Angle : 0.566 9.457 44060 Z= 0.289 Chirality : 0.040 0.161 4924 Planarity : 0.005 0.062 5480 Dihedral : 9.837 124.075 4789 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.08 % Allowed : 11.42 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.14), residues: 3812 helix: 1.73 (0.11), residues: 2464 sheet: -0.22 (0.31), residues: 224 loop : -1.42 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 768 TYR 0.015 0.001 TYR B 380 PHE 0.036 0.001 PHE A 913 TRP 0.011 0.001 TRP A 763 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00340 (32576) covalent geometry : angle 0.56559 (44060) hydrogen bonds : bond 0.05713 ( 1741) hydrogen bonds : angle 3.78281 ( 5149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 411 time to evaluate : 1.206 Fit side-chains REVERT: A 154 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8439 (mppt) REVERT: A 768 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7893 (ttp-110) REVERT: B 169 LEU cc_start: 0.7750 (mt) cc_final: 0.7511 (mp) REVERT: B 176 GLU cc_start: 0.6143 (mp0) cc_final: 0.5826 (mp0) REVERT: B 633 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.5668 (t-90) REVERT: B 1064 ASP cc_start: 0.6407 (t70) cc_final: 0.5873 (t0) REVERT: C 172 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6855 (tp) REVERT: C 365 ASP cc_start: 0.6295 (t0) cc_final: 0.5872 (t0) REVERT: C 413 LEU cc_start: 0.5106 (OUTLIER) cc_final: 0.4562 (mt) REVERT: C 422 LYS cc_start: 0.6518 (mttt) cc_final: 0.6271 (mmtt) REVERT: C 768 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7740 (ttm-80) REVERT: D 235 ASP cc_start: 0.7585 (m-30) cc_final: 0.7103 (m-30) REVERT: D 442 LEU cc_start: 0.8044 (mm) cc_final: 0.7657 (tp) REVERT: D 768 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7728 (ttm-80) REVERT: D 918 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6675 (tt0) outliers start: 71 outliers final: 30 residues processed: 457 average time/residue: 0.7636 time to fit residues: 406.5444 Evaluate side-chains 407 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 374 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 48 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 381 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 360 optimal weight: 0.8980 chunk 226 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 355 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 531 HIS A1135 GLN B 531 HIS C 531 HIS C 539 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.162980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121679 restraints weight = 85125.260| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.12 r_work: 0.3319 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32576 Z= 0.116 Angle : 0.524 9.046 44060 Z= 0.268 Chirality : 0.038 0.139 4924 Planarity : 0.004 0.057 5480 Dihedral : 9.305 109.944 4781 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.84 % Allowed : 12.50 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3812 helix: 1.95 (0.11), residues: 2456 sheet: -0.09 (0.31), residues: 224 loop : -1.32 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 530 TYR 0.012 0.001 TYR D1048 PHE 0.028 0.001 PHE A 913 TRP 0.011 0.001 TRP A 763 HIS 0.004 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00254 (32576) covalent geometry : angle 0.52401 (44060) hydrogen bonds : bond 0.04863 ( 1741) hydrogen bonds : angle 3.50516 ( 5149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 404 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7142 (tp) cc_final: 0.6872 (tp) REVERT: A 768 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7795 (ttp-110) REVERT: A 918 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6650 (tt0) REVERT: A 940 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: B 169 LEU cc_start: 0.7754 (mt) cc_final: 0.7517 (mp) REVERT: B 176 GLU cc_start: 0.6397 (mp0) cc_final: 0.6078 (mp0) REVERT: B 374 LEU cc_start: 0.6643 (mt) cc_final: 0.6314 (mt) REVERT: B 633 HIS cc_start: 0.6539 (OUTLIER) cc_final: 0.5562 (t-90) REVERT: B 768 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7781 (ttm-80) REVERT: B 775 LEU cc_start: 0.8011 (mp) cc_final: 0.7752 (mt) REVERT: B 918 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6794 (tt0) REVERT: B 1064 ASP cc_start: 0.6251 (t70) cc_final: 0.5768 (t0) REVERT: C 172 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6897 (tp) REVERT: C 183 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7233 (mmtp) REVERT: C 413 LEU cc_start: 0.5210 (OUTLIER) cc_final: 0.4669 (mt) REVERT: C 422 LYS cc_start: 0.6569 (mttt) cc_final: 0.6224 (mmtp) REVERT: C 530 ARG cc_start: 0.7153 (mmt180) cc_final: 0.6951 (mmt90) REVERT: C 768 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7828 (ttp-110) REVERT: C 793 LYS cc_start: 0.6491 (mttt) cc_final: 0.5838 (mttp) REVERT: D 231 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6648 (ttp-110) REVERT: D 235 ASP cc_start: 0.7424 (m-30) cc_final: 0.6931 (m-30) REVERT: D 768 ARG cc_start: 0.7990 (ttp-110) cc_final: 0.7605 (ttm-80) REVERT: D 793 LYS cc_start: 0.6258 (mttt) cc_final: 0.5703 (mttp) outliers start: 63 outliers final: 25 residues processed: 449 average time/residue: 0.7713 time to fit residues: 403.4717 Evaluate side-chains 413 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 383 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 60 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 316 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS B 531 HIS C 531 HIS D 288 ASN D 531 HIS D1115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116761 restraints weight = 72411.910| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.78 r_work: 0.3257 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 32576 Z= 0.225 Angle : 0.616 8.915 44060 Z= 0.317 Chirality : 0.043 0.146 4924 Planarity : 0.005 0.097 5480 Dihedral : 9.319 103.606 4780 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.31 % Allowed : 13.15 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3812 helix: 1.62 (0.11), residues: 2484 sheet: -0.31 (0.31), residues: 224 loop : -1.49 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 354 TYR 0.018 0.002 TYR D 878 PHE 0.029 0.002 PHE A 913 TRP 0.013 0.002 TRP B 763 HIS 0.005 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00552 (32576) covalent geometry : angle 0.61574 (44060) hydrogen bonds : bond 0.06760 ( 1741) hydrogen bonds : angle 3.71667 ( 5149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 382 time to evaluate : 1.473 Fit side-chains REVERT: A 350 LEU cc_start: 0.7216 (tp) cc_final: 0.6958 (tp) REVERT: A 768 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7980 (ttp-110) REVERT: A 940 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: B 169 LEU cc_start: 0.7748 (mt) cc_final: 0.7498 (mp) REVERT: B 176 GLU cc_start: 0.6535 (mp0) cc_final: 0.6231 (mp0) REVERT: B 374 LEU cc_start: 0.6755 (mt) cc_final: 0.6418 (mt) REVERT: B 633 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.5736 (t-90) REVERT: B 1064 ASP cc_start: 0.6543 (t70) cc_final: 0.5998 (t0) REVERT: C 372 ASP cc_start: 0.6415 (OUTLIER) cc_final: 0.6211 (m-30) REVERT: C 413 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4543 (mt) REVERT: C 768 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7795 (ttp-110) REVERT: C 791 GLU cc_start: 0.7327 (pm20) cc_final: 0.7047 (pm20) REVERT: C 793 LYS cc_start: 0.6336 (mttt) cc_final: 0.5611 (mttp) REVERT: C 918 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6920 (tt0) REVERT: D 235 ASP cc_start: 0.7568 (m-30) cc_final: 0.7088 (m-30) REVERT: D 768 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7699 (ttm-80) REVERT: D 918 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6808 (tt0) outliers start: 79 outliers final: 35 residues processed: 437 average time/residue: 0.7749 time to fit residues: 395.2733 Evaluate side-chains 413 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 374 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 917 ILE Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 259 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 381 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 81 optimal weight: 4.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 HIS C 531 HIS D 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119450 restraints weight = 71569.067| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.81 r_work: 0.3305 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32576 Z= 0.140 Angle : 0.544 9.224 44060 Z= 0.281 Chirality : 0.040 0.145 4924 Planarity : 0.005 0.080 5480 Dihedral : 8.944 94.497 4779 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.87 % Allowed : 14.06 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.14), residues: 3812 helix: 1.91 (0.11), residues: 2452 sheet: -0.17 (0.31), residues: 224 loop : -1.37 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 530 TYR 0.013 0.001 TYR D1048 PHE 0.027 0.002 PHE A 913 TRP 0.012 0.001 TRP D 763 HIS 0.004 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00325 (32576) covalent geometry : angle 0.54396 (44060) hydrogen bonds : bond 0.05430 ( 1741) hydrogen bonds : angle 3.53571 ( 5149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 381 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7223 (tp) cc_final: 0.6964 (tp) REVERT: A 768 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7984 (ttp-110) REVERT: A 918 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6788 (tt0) REVERT: A 940 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: B 169 LEU cc_start: 0.7709 (mt) cc_final: 0.7470 (mp) REVERT: B 176 GLU cc_start: 0.6622 (mp0) cc_final: 0.6295 (mp0) REVERT: B 372 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6258 (m-30) REVERT: B 374 LEU cc_start: 0.6744 (mt) cc_final: 0.6413 (mt) REVERT: B 442 LEU cc_start: 0.7990 (mm) cc_final: 0.7608 (tp) REVERT: B 633 HIS cc_start: 0.6655 (OUTLIER) cc_final: 0.5606 (t-90) REVERT: B 1064 ASP cc_start: 0.6518 (t70) cc_final: 0.6007 (t0) REVERT: C 169 LEU cc_start: 0.7808 (mp) cc_final: 0.7559 (mp) REVERT: C 183 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7469 (mmtp) REVERT: C 413 LEU cc_start: 0.5194 (OUTLIER) cc_final: 0.4583 (mt) REVERT: C 530 ARG cc_start: 0.7246 (mmt180) cc_final: 0.7027 (mmt90) REVERT: C 768 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7781 (ttp-110) REVERT: C 793 LYS cc_start: 0.6404 (mttt) cc_final: 0.5703 (mttp) REVERT: C 1156 MET cc_start: 0.2735 (mmm) cc_final: 0.2513 (mpm) REVERT: D 235 ASP cc_start: 0.7556 (m-30) cc_final: 0.7091 (m-30) REVERT: D 768 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7634 (ttm-80) REVERT: D 793 LYS cc_start: 0.6292 (mttt) cc_final: 0.5562 (mttp) REVERT: D 918 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6833 (tt0) outliers start: 64 outliers final: 39 residues processed: 427 average time/residue: 0.7770 time to fit residues: 386.2010 Evaluate side-chains 414 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 370 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 367 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 304 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A1135 GLN A1229 ASN B 531 HIS C 531 HIS D 531 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122324 restraints weight = 78337.160| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.43 r_work: 0.3149 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32576 Z= 0.188 Angle : 0.579 8.901 44060 Z= 0.301 Chirality : 0.041 0.144 4924 Planarity : 0.005 0.082 5480 Dihedral : 8.858 90.729 4777 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.96 % Allowed : 14.03 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.14), residues: 3812 helix: 1.77 (0.11), residues: 2456 sheet: -0.31 (0.30), residues: 224 loop : -1.45 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 530 TYR 0.015 0.002 TYR D 878 PHE 0.028 0.002 PHE B 913 TRP 0.013 0.002 TRP B 763 HIS 0.004 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00456 (32576) covalent geometry : angle 0.57929 (44060) hydrogen bonds : bond 0.06133 ( 1741) hydrogen bonds : angle 3.59777 ( 5149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 371 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7599 (tp) cc_final: 0.7315 (tp) REVERT: A 587 ASN cc_start: 0.7147 (p0) cc_final: 0.6830 (p0) REVERT: A 918 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7121 (tt0) REVERT: B 169 LEU cc_start: 0.8175 (mt) cc_final: 0.7957 (mp) REVERT: B 176 GLU cc_start: 0.6853 (mp0) cc_final: 0.6622 (mp0) REVERT: B 633 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.5606 (t-90) REVERT: B 768 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7990 (ttm-80) REVERT: B 1064 ASP cc_start: 0.6591 (t70) cc_final: 0.6196 (t0) REVERT: C 183 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7688 (mmtp) REVERT: C 413 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4700 (mt) REVERT: C 793 LYS cc_start: 0.6696 (mttt) cc_final: 0.5950 (mttp) REVERT: C 918 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7200 (tt0) REVERT: C 1156 MET cc_start: 0.2907 (mmm) cc_final: 0.2676 (mpm) REVERT: D 172 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7508 (tp) REVERT: D 235 ASP cc_start: 0.7899 (m-30) cc_final: 0.7497 (m-30) REVERT: D 421 MET cc_start: 0.7438 (tpp) cc_final: 0.7116 (mmm) REVERT: D 768 ARG cc_start: 0.8018 (ttp-110) cc_final: 0.7681 (ttm-80) REVERT: D 793 LYS cc_start: 0.6669 (mttt) cc_final: 0.6467 (mtmm) outliers start: 67 outliers final: 41 residues processed: 422 average time/residue: 0.7582 time to fit residues: 373.2207 Evaluate side-chains 411 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 1061 ASP Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 917 ILE Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 372 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A1135 GLN A1229 ASN B 531 HIS C 531 HIS D 531 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.155779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120758 restraints weight = 72346.079| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.14 r_work: 0.3134 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 32576 Z= 0.273 Angle : 0.665 9.165 44060 Z= 0.345 Chirality : 0.045 0.159 4924 Planarity : 0.005 0.094 5480 Dihedral : 9.135 89.543 4777 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.90 % Allowed : 14.38 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.13), residues: 3812 helix: 1.47 (0.10), residues: 2452 sheet: -0.56 (0.30), residues: 224 loop : -1.60 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 768 TYR 0.018 0.002 TYR C 981 PHE 0.033 0.002 PHE B1047 TRP 0.015 0.002 TRP C 256 HIS 0.005 0.001 HIS B 752 Details of bonding type rmsd covalent geometry : bond 0.00674 (32576) covalent geometry : angle 0.66523 (44060) hydrogen bonds : bond 0.07302 ( 1741) hydrogen bonds : angle 3.80089 ( 5149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7690 (tp) cc_final: 0.7416 (tp) REVERT: A 587 ASN cc_start: 0.7179 (p0) cc_final: 0.6936 (p0) REVERT: A 715 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8565 (mtpt) REVERT: A 768 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7897 (ttp-110) REVERT: A 918 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7176 (tt0) REVERT: B 169 LEU cc_start: 0.8250 (mt) cc_final: 0.8017 (mp) REVERT: B 633 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.5640 (t-90) REVERT: C 397 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6573 (p) REVERT: C 413 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.4794 (mt) REVERT: C 587 ASN cc_start: 0.6937 (p0) cc_final: 0.6426 (p0) REVERT: C 768 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7771 (ttm-80) REVERT: C 775 LEU cc_start: 0.8116 (mt) cc_final: 0.7770 (mp) REVERT: D 172 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7574 (tp) REVERT: D 235 ASP cc_start: 0.7966 (m-30) cc_final: 0.7644 (m-30) REVERT: D 768 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7702 (ttm-80) REVERT: D 918 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7096 (tt0) outliers start: 65 outliers final: 42 residues processed: 426 average time/residue: 0.7643 time to fit residues: 377.8517 Evaluate side-chains 414 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 368 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1061 ASP Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 917 ILE Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 206 optimal weight: 0.8980 chunk 40 optimal weight: 0.0170 chunk 95 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 328 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 284 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A1229 ASN B 531 HIS C 531 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.160753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123442 restraints weight = 59844.669| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.34 r_work: 0.3241 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32576 Z= 0.118 Angle : 0.540 10.361 44060 Z= 0.278 Chirality : 0.039 0.135 4924 Planarity : 0.005 0.069 5480 Dihedral : 8.375 76.926 4777 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.41 % Allowed : 14.99 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.14), residues: 3812 helix: 1.94 (0.11), residues: 2460 sheet: -0.22 (0.31), residues: 224 loop : -1.39 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 768 TYR 0.014 0.001 TYR D1048 PHE 0.029 0.001 PHE D1047 TRP 0.011 0.001 TRP D 763 HIS 0.004 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00257 (32576) covalent geometry : angle 0.53964 (44060) hydrogen bonds : bond 0.04890 ( 1741) hydrogen bonds : angle 3.47082 ( 5149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 383 time to evaluate : 1.229 Fit side-chains REVERT: A 350 LEU cc_start: 0.7634 (tp) cc_final: 0.7347 (tp) REVERT: A 587 ASN cc_start: 0.7141 (p0) cc_final: 0.6914 (p0) REVERT: A 685 ASN cc_start: 0.7065 (m-40) cc_final: 0.6589 (t0) REVERT: A 768 ARG cc_start: 0.8331 (ttm110) cc_final: 0.8041 (ttp-110) REVERT: A 918 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7161 (tt0) REVERT: B 169 LEU cc_start: 0.8167 (mt) cc_final: 0.7915 (mp) REVERT: B 176 GLU cc_start: 0.6445 (mp0) cc_final: 0.6204 (mp0) REVERT: B 633 HIS cc_start: 0.6718 (OUTLIER) cc_final: 0.5686 (t-90) REVERT: B 793 LYS cc_start: 0.6517 (mttt) cc_final: 0.5783 (mttp) REVERT: B 918 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7213 (tt0) REVERT: B 1064 ASP cc_start: 0.6544 (t70) cc_final: 0.6297 (t0) REVERT: C 151 HIS cc_start: 0.6152 (OUTLIER) cc_final: 0.5772 (p90) REVERT: C 183 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7751 (mmtp) REVERT: C 413 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4503 (mt) REVERT: C 587 ASN cc_start: 0.6962 (p0) cc_final: 0.6476 (p0) REVERT: C 768 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7926 (ttp-110) REVERT: C 793 LYS cc_start: 0.6566 (mttt) cc_final: 0.5916 (mttp) REVERT: C 932 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7352 (tt) REVERT: D 172 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7626 (tp) REVERT: D 173 MET cc_start: 0.8080 (mtp) cc_final: 0.7785 (mtm) REVERT: D 231 ARG cc_start: 0.7725 (ttp-110) cc_final: 0.7256 (mtp-110) REVERT: D 235 ASP cc_start: 0.8051 (m-30) cc_final: 0.7651 (m-30) REVERT: D 421 MET cc_start: 0.7438 (tpp) cc_final: 0.7081 (mmm) REVERT: D 768 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7706 (ttm-80) REVERT: D 918 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7063 (tt0) outliers start: 48 outliers final: 31 residues processed: 419 average time/residue: 0.8024 time to fit residues: 390.3914 Evaluate side-chains 403 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 366 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 917 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 249 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 349 optimal weight: 6.9990 chunk 88 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 380 optimal weight: 7.9990 chunk 251 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A1135 GLN A1229 ASN B 531 HIS C 531 HIS D 531 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116469 restraints weight = 80942.625| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.87 r_work: 0.3212 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32576 Z= 0.124 Angle : 0.540 10.957 44060 Z= 0.279 Chirality : 0.039 0.172 4924 Planarity : 0.005 0.066 5480 Dihedral : 8.221 73.607 4777 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.32 % Allowed : 15.37 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.14), residues: 3812 helix: 2.03 (0.11), residues: 2460 sheet: -0.10 (0.31), residues: 224 loop : -1.32 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 768 TYR 0.013 0.001 TYR D1048 PHE 0.029 0.001 PHE A1047 TRP 0.013 0.001 TRP C 763 HIS 0.004 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00280 (32576) covalent geometry : angle 0.54048 (44060) hydrogen bonds : bond 0.04918 ( 1741) hydrogen bonds : angle 3.43612 ( 5149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 371 time to evaluate : 1.263 Fit side-chains REVERT: A 350 LEU cc_start: 0.7551 (tp) cc_final: 0.7272 (tp) REVERT: A 587 ASN cc_start: 0.7047 (p0) cc_final: 0.6829 (p0) REVERT: A 685 ASN cc_start: 0.7049 (m-40) cc_final: 0.6628 (t0) REVERT: A 768 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7914 (ttp-110) REVERT: A 918 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7017 (tt0) REVERT: B 169 LEU cc_start: 0.8127 (mt) cc_final: 0.7920 (mp) REVERT: B 633 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.5467 (t-90) REVERT: B 793 LYS cc_start: 0.6480 (mttt) cc_final: 0.5807 (mttp) REVERT: B 918 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7000 (tt0) REVERT: B 1064 ASP cc_start: 0.6419 (t70) cc_final: 0.6199 (t0) REVERT: C 151 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.5853 (p90) REVERT: C 183 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7687 (mmtp) REVERT: C 413 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.4542 (mt) REVERT: C 587 ASN cc_start: 0.7024 (p0) cc_final: 0.6551 (p0) REVERT: C 768 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7640 (ttm-80) REVERT: C 793 LYS cc_start: 0.6626 (mttt) cc_final: 0.6043 (mttp) REVERT: D 172 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7607 (tp) REVERT: D 173 MET cc_start: 0.8013 (mtp) cc_final: 0.7734 (mtm) REVERT: D 231 ARG cc_start: 0.7502 (ttp-110) cc_final: 0.6992 (mtp-110) REVERT: D 235 ASP cc_start: 0.7820 (m-30) cc_final: 0.7429 (m-30) REVERT: D 421 MET cc_start: 0.7471 (tpp) cc_final: 0.7137 (mmm) REVERT: D 768 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7599 (ttm-80) REVERT: D 918 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6948 (tt0) outliers start: 45 outliers final: 33 residues processed: 407 average time/residue: 0.7840 time to fit residues: 371.2649 Evaluate side-chains 400 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 362 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 1061 ASP Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain C residue 1061 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 917 ILE Chi-restraints excluded: chain D residue 1061 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 326 optimal weight: 0.9990 chunk 289 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A1229 ASN B 279 ASN B 314 GLN B 531 HIS C 531 HIS C1135 GLN D 531 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124263 restraints weight = 56779.027| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.31 r_work: 0.3173 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 32576 Z= 0.190 Angle : 0.601 17.554 44060 Z= 0.309 Chirality : 0.041 0.174 4924 Planarity : 0.005 0.079 5480 Dihedral : 8.393 76.854 4777 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.29 % Allowed : 15.61 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3812 helix: 1.82 (0.11), residues: 2452 sheet: -0.27 (0.31), residues: 224 loop : -1.43 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 768 TYR 0.014 0.002 TYR D 878 PHE 0.031 0.002 PHE B1047 TRP 0.015 0.002 TRP B 763 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00462 (32576) covalent geometry : angle 0.60150 (44060) hydrogen bonds : bond 0.06086 ( 1741) hydrogen bonds : angle 3.57804 ( 5149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 364 time to evaluate : 1.258 Fit side-chains REVERT: A 350 LEU cc_start: 0.7612 (tp) cc_final: 0.7323 (tp) REVERT: A 587 ASN cc_start: 0.7110 (p0) cc_final: 0.6898 (p0) REVERT: A 685 ASN cc_start: 0.7169 (m-40) cc_final: 0.6726 (t0) REVERT: A 768 ARG cc_start: 0.8212 (ttm110) cc_final: 0.7914 (ttp-110) REVERT: A 918 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7102 (tt0) REVERT: B 169 LEU cc_start: 0.8180 (mt) cc_final: 0.7945 (mp) REVERT: B 633 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.5621 (t-90) REVERT: B 918 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7101 (tt0) REVERT: B 1064 ASP cc_start: 0.6436 (t70) cc_final: 0.6230 (t0) REVERT: C 151 HIS cc_start: 0.6269 (OUTLIER) cc_final: 0.5867 (p90) REVERT: C 413 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4606 (mt) REVERT: C 482 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 768 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7663 (ttm-80) REVERT: C 793 LYS cc_start: 0.6587 (mttt) cc_final: 0.5953 (mttp) REVERT: D 172 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7641 (tp) REVERT: D 231 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7103 (mtp-110) REVERT: D 235 ASP cc_start: 0.7892 (m-30) cc_final: 0.7514 (m-30) REVERT: D 421 MET cc_start: 0.7504 (tpp) cc_final: 0.7186 (mmm) REVERT: D 768 ARG cc_start: 0.7958 (ttp-110) cc_final: 0.7695 (ttm-80) REVERT: D 918 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7034 (tt0) outliers start: 44 outliers final: 33 residues processed: 399 average time/residue: 0.7667 time to fit residues: 356.7266 Evaluate side-chains 398 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 361 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain B residue 1061 ASP Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 1041 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 917 ILE Chi-restraints excluded: chain D residue 1061 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 190 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 247 optimal weight: 0.9980 chunk 305 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 386 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A1229 ASN B 531 HIS C 531 HIS D 531 HIS D1135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.160190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123248 restraints weight = 66487.430| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.67 r_work: 0.3229 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32576 Z= 0.125 Angle : 0.563 16.132 44060 Z= 0.287 Chirality : 0.039 0.162 4924 Planarity : 0.005 0.073 5480 Dihedral : 8.183 72.766 4777 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.23 % Allowed : 15.64 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.14), residues: 3812 helix: 2.01 (0.11), residues: 2456 sheet: -0.12 (0.31), residues: 224 loop : -1.36 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 768 TYR 0.013 0.001 TYR D1048 PHE 0.030 0.001 PHE D1047 TRP 0.014 0.001 TRP B 763 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00276 (32576) covalent geometry : angle 0.56330 (44060) hydrogen bonds : bond 0.05186 ( 1741) hydrogen bonds : angle 3.48902 ( 5149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13517.09 seconds wall clock time: 230 minutes 14.72 seconds (13814.72 seconds total)