Starting phenix.real_space_refine on Fri Jun 27 23:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddq_27338/06_2025/8ddq_27338.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddq_27338/06_2025/8ddq_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_27338/06_2025/8ddq_27338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddq_27338/06_2025/8ddq_27338.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddq_27338/06_2025/8ddq_27338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddq_27338/06_2025/8ddq_27338.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 1.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 35.72, per 1000 atoms: 1.12 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: 7.66 Conformation dependent library (CDL) restraints added in 7.5 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: 3.59 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: 13.22 Time building geometry restraints manager: 9.23 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: 4.810 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: 1.480 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 94.530 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (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 TRP 0.012 0.001 TRP A 763 HIS 0.003 0.001 HIS C 412 PHE 0.009 0.001 PHE C 913 TYR 0.014 0.001 TYR C1048 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.15212 ( 1741) hydrogen bonds : angle 4.80973 ( 5149) covalent geometry : bond 0.01500 (32576) covalent geometry : angle 0.96191 (44060) *********************** 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 : 3.385 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: 0.2681 (mpm) REVERT: C 413 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5421 (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: 0.8299 (m-40) outliers start: 55 outliers final: 16 residues processed: 551 average time/residue: 1.5358 time to fit residues: 991.7399 Evaluate side-chains 404 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 384 time to evaluate : 3.525 ------------------------------------------------------------------------------- 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 327 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 171 HIS 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118769 restraints weight = 74147.395| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.84 r_work: 0.3291 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 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 = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32576 Z= 0.177 Angle : 0.592 9.680 44060 Z= 0.303 Chirality : 0.041 0.173 4924 Planarity : 0.005 0.066 5480 Dihedral : 9.939 125.161 4789 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.05 % Allowed : 11.63 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3812 helix: 1.56 (0.11), residues: 2476 sheet: -0.29 (0.31), residues: 224 loop : -1.47 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 763 HIS 0.004 0.001 HIS D 412 PHE 0.037 0.002 PHE A 913 TYR 0.016 0.002 TYR B 380 ARG 0.010 0.001 ARG C 768 Details of bonding type rmsd hydrogen bonds : bond 0.06214 ( 1741) hydrogen bonds : angle 3.84878 ( 5149) covalent geometry : bond 0.00425 (32576) covalent geometry : angle 0.59190 (44060) *********************** 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 468 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 398 time to evaluate : 3.681 Fit side-chains REVERT: A 154 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8441 (mppt) REVERT: A 768 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7911 (ttp-110) REVERT: B 169 LEU cc_start: 0.7737 (mt) cc_final: 0.7502 (mp) REVERT: B 176 GLU cc_start: 0.6166 (mp0) cc_final: 0.5851 (mp0) REVERT: B 633 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.5707 (t-90) REVERT: B 1064 ASP cc_start: 0.6493 (t70) cc_final: 0.5955 (t0) REVERT: C 365 ASP cc_start: 0.6302 (t0) cc_final: 0.5881 (t0) REVERT: C 413 LEU cc_start: 0.5165 (OUTLIER) cc_final: 0.4604 (mt) REVERT: C 422 LYS cc_start: 0.6513 (mttt) cc_final: 0.6264 (mmtt) REVERT: C 768 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7766 (ttm-80) REVERT: D 235 ASP cc_start: 0.7616 (m-30) cc_final: 0.7139 (m-30) REVERT: D 768 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7775 (ttm-80) REVERT: D 918 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6764 (tt0) outliers start: 70 outliers final: 28 residues processed: 445 average time/residue: 1.5422 time to fit residues: 803.1689 Evaluate side-chains 405 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 375 time to evaluate : 3.464 ------------------------------------------------------------------------------- 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 204 VAL 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 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 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 1191 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 131 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 370 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 0.0000 chunk 38 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A1135 GLN B 531 HIS C 531 HIS D 288 ASN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.160104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118462 restraints weight = 78889.115| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.82 r_work: 0.3284 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32576 Z= 0.158 Angle : 0.563 9.093 44060 Z= 0.289 Chirality : 0.040 0.155 4924 Planarity : 0.005 0.068 5480 Dihedral : 9.552 114.269 4781 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.14 % Allowed : 12.30 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3812 helix: 1.68 (0.11), residues: 2476 sheet: -0.23 (0.31), residues: 224 loop : -1.46 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 763 HIS 0.005 0.001 HIS D 412 PHE 0.030 0.002 PHE A 913 TYR 0.014 0.002 TYR D 878 ARG 0.008 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.05810 ( 1741) hydrogen bonds : angle 3.65478 ( 5149) covalent geometry : bond 0.00374 (32576) covalent geometry : angle 0.56287 (44060) *********************** 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 458 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 385 time to evaluate : 3.517 Fit side-chains REVERT: A 172 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6709 (tp) REVERT: A 768 ARG cc_start: 0.8275 (ttm110) cc_final: 0.8061 (ttp-110) REVERT: A 918 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6823 (tt0) REVERT: A 932 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6137 (tt) REVERT: A 940 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: B 169 LEU cc_start: 0.7750 (mt) cc_final: 0.7514 (mp) REVERT: B 176 GLU cc_start: 0.6373 (mp0) cc_final: 0.6136 (mp0) REVERT: B 633 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.5699 (t-90) REVERT: B 768 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7907 (ttm-80) REVERT: B 775 LEU cc_start: 0.7955 (mp) cc_final: 0.7703 (mt) REVERT: B 1064 ASP cc_start: 0.6504 (t70) cc_final: 0.5961 (t0) REVERT: C 183 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7412 (mmtp) REVERT: C 413 LEU cc_start: 0.5202 (OUTLIER) cc_final: 0.4647 (mt) REVERT: C 768 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7913 (ttp-110) REVERT: D 192 LEU cc_start: 0.7171 (pt) cc_final: 0.6935 (pp) REVERT: D 231 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.6896 (ttp-110) REVERT: D 235 ASP cc_start: 0.7656 (m-30) cc_final: 0.7176 (m-30) REVERT: D 768 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7699 (ttm-80) outliers start: 73 outliers final: 35 residues processed: 437 average time/residue: 1.5010 time to fit residues: 770.9733 Evaluate side-chains 416 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 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 932 LEU 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 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 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 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 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 917 ILE 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 385 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 295 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 375 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 GLN A1229 ASN B 531 HIS C 531 HIS C 539 HIS D 531 HIS D1115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118793 restraints weight = 64043.302| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.57 r_work: 0.3310 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32576 Z= 0.166 Angle : 0.563 9.064 44060 Z= 0.289 Chirality : 0.040 0.145 4924 Planarity : 0.005 0.070 5480 Dihedral : 9.241 103.331 4781 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.11 % Allowed : 13.03 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3812 helix: 1.75 (0.11), residues: 2456 sheet: -0.22 (0.31), residues: 224 loop : -1.41 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 763 HIS 0.005 0.001 HIS C 531 PHE 0.029 0.002 PHE A 913 TYR 0.014 0.002 TYR D 878 ARG 0.006 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.05859 ( 1741) hydrogen bonds : angle 3.59920 ( 5149) covalent geometry : bond 0.00397 (32576) covalent geometry : angle 0.56303 (44060) *********************** 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 452 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 380 time to evaluate : 3.953 Fit side-chains REVERT: A 154 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8490 (mppt) REVERT: A 172 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6726 (tp) REVERT: A 768 ARG cc_start: 0.8252 (ttm110) cc_final: 0.8007 (ttp-110) REVERT: A 918 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6782 (tt0) REVERT: A 940 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: B 169 LEU cc_start: 0.7662 (mt) cc_final: 0.7406 (mp) REVERT: B 176 GLU cc_start: 0.6544 (mp0) cc_final: 0.6250 (mp0) REVERT: B 372 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6339 (m-30) REVERT: B 374 LEU cc_start: 0.6852 (mt) cc_final: 0.6500 (mt) REVERT: B 633 HIS cc_start: 0.6697 (OUTLIER) cc_final: 0.5665 (t-90) REVERT: B 775 LEU cc_start: 0.7925 (mp) cc_final: 0.7688 (mt) REVERT: B 793 LYS cc_start: 0.6441 (mttt) cc_final: 0.6228 (mtmt) REVERT: B 1064 ASP cc_start: 0.6503 (t70) cc_final: 0.5976 (t0) REVERT: C 413 LEU cc_start: 0.5111 (OUTLIER) cc_final: 0.4514 (mt) REVERT: C 768 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7803 (ttp-110) REVERT: C 793 LYS cc_start: 0.6298 (mttt) cc_final: 0.5606 (mttp) REVERT: D 192 LEU cc_start: 0.7165 (pt) cc_final: 0.6926 (pp) REVERT: D 231 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.6800 (ttp-110) REVERT: D 235 ASP cc_start: 0.7572 (m-30) cc_final: 0.7095 (m-30) REVERT: D 768 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7676 (ttm-80) REVERT: D 918 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6821 (tt0) outliers start: 72 outliers final: 37 residues processed: 428 average time/residue: 1.6031 time to fit residues: 806.7427 Evaluate side-chains 417 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 375 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 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 932 LEU 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 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 440 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 373 ILE Chi-restraints excluded: chain C residue 403 PHE 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 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 1191 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 295 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 363 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 327 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1229 ASN B 531 HIS C 531 HIS D 531 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120183 restraints weight = 68417.575| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.67 r_work: 0.3316 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32576 Z= 0.139 Angle : 0.537 9.283 44060 Z= 0.277 Chirality : 0.039 0.152 4924 Planarity : 0.004 0.068 5480 Dihedral : 8.864 93.275 4780 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.05 % Allowed : 13.47 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.14), residues: 3812 helix: 1.92 (0.11), residues: 2452 sheet: -0.16 (0.31), residues: 224 loop : -1.36 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 763 HIS 0.004 0.001 HIS C 531 PHE 0.027 0.002 PHE A 913 TYR 0.012 0.001 TYR D 878 ARG 0.006 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.05306 ( 1741) hydrogen bonds : angle 3.49036 ( 5149) covalent geometry : bond 0.00321 (32576) covalent geometry : angle 0.53742 (44060) *********************** 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 461 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 391 time to evaluate : 3.921 Fit side-chains REVERT: A 154 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8477 (mppt) REVERT: A 587 ASN cc_start: 0.7133 (p0) cc_final: 0.6728 (p0) REVERT: A 768 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7860 (ttp-110) REVERT: A 940 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: B 169 LEU cc_start: 0.7760 (mt) cc_final: 0.7526 (mp) REVERT: B 176 GLU cc_start: 0.6678 (mp0) cc_final: 0.6379 (mp0) REVERT: B 231 ARG cc_start: 0.7349 (ttp-110) cc_final: 0.7071 (mtp-110) REVERT: B 372 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6349 (m-30) REVERT: B 633 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.5615 (t-90) REVERT: B 775 LEU cc_start: 0.7933 (mp) cc_final: 0.7677 (mt) REVERT: B 1064 ASP cc_start: 0.6540 (t70) cc_final: 0.6036 (t0) REVERT: C 169 LEU cc_start: 0.7851 (mp) cc_final: 0.7602 (mp) REVERT: C 183 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7484 (mmtp) REVERT: C 413 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4604 (mt) REVERT: C 530 ARG cc_start: 0.7245 (mmt180) cc_final: 0.7031 (mmt90) REVERT: C 768 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7780 (ttp-110) REVERT: C 1156 MET cc_start: 0.2693 (mmm) cc_final: 0.2459 (mpm) REVERT: D 192 LEU cc_start: 0.7153 (pt) cc_final: 0.6911 (pp) REVERT: D 231 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.6859 (ttp-110) REVERT: D 235 ASP cc_start: 0.7633 (m-30) cc_final: 0.7154 (m-30) REVERT: D 768 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7645 (ttm-80) REVERT: D 918 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6904 (tt0) outliers start: 70 outliers final: 43 residues processed: 435 average time/residue: 1.7087 time to fit residues: 875.5136 Evaluate side-chains 417 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 369 time to evaluate : 3.668 ------------------------------------------------------------------------------- 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 932 LEU Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1022 MET 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 283 LYS 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 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 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 1185 ILE 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 93 optimal weight: 0.8980 chunk 330 optimal weight: 0.9980 chunk 170 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 157 optimal weight: 0.0070 chunk 252 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.163970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123342 restraints weight = 70620.872| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.69 r_work: 0.3344 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32576 Z= 0.103 Angle : 0.499 9.303 44060 Z= 0.256 Chirality : 0.038 0.144 4924 Planarity : 0.004 0.055 5480 Dihedral : 8.289 78.952 4778 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.67 % Allowed : 14.17 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.14), residues: 3812 helix: 2.19 (0.11), residues: 2444 sheet: 0.04 (0.31), residues: 224 loop : -1.22 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 763 HIS 0.004 0.001 HIS D 240 PHE 0.027 0.001 PHE A 913 TYR 0.013 0.001 TYR D1048 ARG 0.006 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1741) hydrogen bonds : angle 3.31523 ( 5149) covalent geometry : bond 0.00214 (32576) covalent geometry : angle 0.49898 (44060) *********************** 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 450 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 393 time to evaluate : 6.487 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8458 (mppt) REVERT: A 587 ASN cc_start: 0.6951 (p0) cc_final: 0.6563 (p0) REVERT: A 685 ASN cc_start: 0.6660 (m-40) cc_final: 0.6322 (t0) REVERT: A 768 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7887 (ttp-110) REVERT: A 918 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6789 (tt0) REVERT: A 932 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5497 (mm) REVERT: A 940 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: B 169 LEU cc_start: 0.7707 (mt) cc_final: 0.7485 (mp) REVERT: B 176 GLU cc_start: 0.6702 (mp0) cc_final: 0.6417 (mp0) REVERT: B 231 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.6997 (mtp-110) REVERT: B 633 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.5534 (t-90) REVERT: B 768 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7904 (ttm110) REVERT: B 775 LEU cc_start: 0.7892 (mp) cc_final: 0.7637 (mt) REVERT: B 1064 ASP cc_start: 0.6491 (t70) cc_final: 0.6011 (t0) REVERT: C 151 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5632 (p90) REVERT: C 169 LEU cc_start: 0.7857 (mp) cc_final: 0.7587 (mp) REVERT: C 183 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7488 (mmtp) REVERT: C 413 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4520 (mt) REVERT: C 768 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7815 (ttm110) REVERT: C 1156 MET cc_start: 0.2890 (mmm) cc_final: 0.2641 (mpm) REVERT: D 231 ARG cc_start: 0.7343 (ttp-110) cc_final: 0.6713 (ttp-110) REVERT: D 235 ASP cc_start: 0.7528 (m-30) cc_final: 0.7049 (m-30) REVERT: D 374 LEU cc_start: 0.6967 (mt) cc_final: 0.6690 (mt) REVERT: D 421 MET cc_start: 0.7104 (tpp) cc_final: 0.6754 (mmm) REVERT: D 432 MET cc_start: 0.6614 (ttt) cc_final: 0.6386 (ttt) REVERT: D 768 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7626 (ttm-80) REVERT: D 918 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6790 (tt0) REVERT: D 1135 GLN cc_start: 0.8489 (tp40) cc_final: 0.8209 (tp40) outliers start: 57 outliers final: 27 residues processed: 433 average time/residue: 1.7436 time to fit residues: 887.7056 Evaluate side-chains 410 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 377 time to evaluate : 3.687 ------------------------------------------------------------------------------- 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 932 LEU 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 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 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 485 VAL 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 1185 ILE 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 257 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 375 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 289 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 531 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.162167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121017 restraints weight = 88660.255| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.10 r_work: 0.3306 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1567 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= 0.130 Angle : 0.525 9.396 44060 Z= 0.270 Chirality : 0.039 0.148 4924 Planarity : 0.004 0.090 5480 Dihedral : 8.227 74.179 4778 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.55 % Allowed : 14.58 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3812 helix: 2.12 (0.11), residues: 2456 sheet: 0.03 (0.31), residues: 224 loop : -1.23 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 763 HIS 0.004 0.001 HIS D 240 PHE 0.027 0.001 PHE D 913 TYR 0.013 0.001 TYR D1048 ARG 0.008 0.000 ARG C 530 Details of bonding type rmsd hydrogen bonds : bond 0.04928 ( 1741) hydrogen bonds : angle 3.37010 ( 5149) covalent geometry : bond 0.00300 (32576) covalent geometry : angle 0.52473 (44060) *********************** 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 437 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 384 time to evaluate : 3.632 Fit side-chains revert: symmetry clash REVERT: A 587 ASN cc_start: 0.7008 (p0) cc_final: 0.6677 (p0) REVERT: A 685 ASN cc_start: 0.6668 (m-40) cc_final: 0.6342 (t0) REVERT: A 768 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7778 (ttp-110) REVERT: A 918 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6670 (tt0) REVERT: A 932 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5504 (mm) REVERT: A 940 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7348 (mt0) REVERT: B 169 LEU cc_start: 0.7704 (mt) cc_final: 0.7488 (mp) REVERT: B 176 GLU cc_start: 0.6687 (mp0) cc_final: 0.6426 (mp0) REVERT: B 231 ARG cc_start: 0.7067 (ttp-110) cc_final: 0.6776 (mtp-110) REVERT: B 442 LEU cc_start: 0.8010 (mm) cc_final: 0.7604 (tp) REVERT: B 633 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.5399 (t-90) REVERT: B 768 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7810 (ttm110) REVERT: B 1064 ASP cc_start: 0.6368 (t70) cc_final: 0.5894 (t0) REVERT: C 151 HIS cc_start: 0.6099 (OUTLIER) cc_final: 0.5695 (p90) REVERT: C 169 LEU cc_start: 0.7811 (mp) cc_final: 0.7544 (mp) REVERT: C 183 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7408 (mmtp) REVERT: C 413 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4385 (mt) REVERT: C 587 ASN cc_start: 0.6764 (p0) cc_final: 0.6403 (p0) REVERT: C 1156 MET cc_start: 0.2866 (mmm) cc_final: 0.2608 (mpm) REVERT: D 231 ARG cc_start: 0.7212 (ttp-110) cc_final: 0.6578 (ttp-110) REVERT: D 235 ASP cc_start: 0.7377 (m-30) cc_final: 0.6913 (m-30) REVERT: D 374 LEU cc_start: 0.6800 (mt) cc_final: 0.6559 (mt) REVERT: D 421 MET cc_start: 0.7094 (tpp) cc_final: 0.6715 (mmm) REVERT: D 768 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7741 (ttm-80) REVERT: D 1135 GLN cc_start: 0.8291 (tp40) cc_final: 0.8004 (tp40) outliers start: 53 outliers final: 33 residues processed: 421 average time/residue: 1.5655 time to fit residues: 774.7817 Evaluate side-chains 415 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 376 time to evaluate : 3.446 ------------------------------------------------------------------------------- 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 932 LEU 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 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 B residue 1061 ASP 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 449 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 502 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 77 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 342 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 357 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 C1135 GLN D 531 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.162458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121785 restraints weight = 84774.284| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.08 r_work: 0.3285 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32576 Z= 0.123 Angle : 0.522 9.995 44060 Z= 0.269 Chirality : 0.039 0.142 4924 Planarity : 0.004 0.083 5480 Dihedral : 8.153 72.008 4778 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.55 % Allowed : 14.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.14), residues: 3812 helix: 2.14 (0.11), residues: 2456 sheet: 0.07 (0.31), residues: 224 loop : -1.23 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 763 HIS 0.005 0.001 HIS C 240 PHE 0.027 0.001 PHE A 913 TYR 0.012 0.001 TYR D1048 ARG 0.010 0.000 ARG C 768 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 1741) hydrogen bonds : angle 3.35176 ( 5149) covalent geometry : bond 0.00280 (32576) covalent geometry : angle 0.52169 (44060) *********************** 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 433 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 3.686 Fit side-chains revert: symmetry clash REVERT: A 354 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6840 (mtm-85) REVERT: A 685 ASN cc_start: 0.6615 (m-40) cc_final: 0.6298 (t0) REVERT: A 768 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7752 (ttp-110) REVERT: A 918 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6639 (tt0) REVERT: A 932 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5453 (mm) REVERT: A 940 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: B 169 LEU cc_start: 0.7641 (mt) cc_final: 0.7427 (mp) REVERT: B 176 GLU cc_start: 0.6644 (mp0) cc_final: 0.6386 (mp0) REVERT: B 231 ARG cc_start: 0.6970 (ttp-110) cc_final: 0.6666 (mtp-110) REVERT: B 442 LEU cc_start: 0.7929 (mm) cc_final: 0.7525 (tp) REVERT: B 633 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.5408 (t-90) REVERT: B 768 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7790 (ttm110) REVERT: B 1064 ASP cc_start: 0.6361 (t70) cc_final: 0.5881 (t0) REVERT: C 151 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5678 (p90) REVERT: C 169 LEU cc_start: 0.7742 (mp) cc_final: 0.7462 (mp) REVERT: C 183 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7401 (mmtp) REVERT: C 413 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4272 (mt) REVERT: C 587 ASN cc_start: 0.6745 (p0) cc_final: 0.6329 (p0) REVERT: C 1156 MET cc_start: 0.2836 (mmm) cc_final: 0.2575 (mpm) REVERT: D 231 ARG cc_start: 0.7152 (ttp-110) cc_final: 0.6516 (ttp-110) REVERT: D 235 ASP cc_start: 0.7313 (m-30) cc_final: 0.6846 (m-30) REVERT: D 374 LEU cc_start: 0.6727 (mt) cc_final: 0.6481 (mt) REVERT: D 421 MET cc_start: 0.7026 (tpp) cc_final: 0.6660 (mmm) REVERT: D 768 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7728 (ttm-80) REVERT: D 918 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6482 (tt0) REVERT: D 1135 GLN cc_start: 0.8313 (tp40) cc_final: 0.8022 (tp40) outliers start: 53 outliers final: 36 residues processed: 419 average time/residue: 1.5490 time to fit residues: 760.1215 Evaluate side-chains 419 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 3.924 ------------------------------------------------------------------------------- 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 932 LEU 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 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 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 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 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 449 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 502 ASP 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 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 1191 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 202 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 359 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 531 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116627 restraints weight = 80214.094| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.80 r_work: 0.3171 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 32576 Z= 0.219 Angle : 0.603 9.237 44060 Z= 0.313 Chirality : 0.042 0.147 4924 Planarity : 0.005 0.096 5480 Dihedral : 8.495 77.534 4778 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.73 % Allowed : 14.79 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3812 helix: 1.80 (0.11), residues: 2452 sheet: -0.19 (0.31), residues: 224 loop : -1.39 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 763 HIS 0.004 0.001 HIS C 240 PHE 0.030 0.002 PHE D 913 TYR 0.016 0.002 TYR D 878 ARG 0.010 0.001 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.06419 ( 1741) hydrogen bonds : angle 3.58516 ( 5149) covalent geometry : bond 0.00534 (32576) covalent geometry : angle 0.60254 (44060) *********************** 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 430 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 371 time to evaluate : 3.430 Fit side-chains REVERT: A 154 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8603 (mppt) REVERT: A 587 ASN cc_start: 0.7104 (p0) cc_final: 0.6701 (p0) REVERT: A 685 ASN cc_start: 0.7120 (m-40) cc_final: 0.6693 (t0) REVERT: A 918 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7115 (tt0) REVERT: A 932 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5858 (mm) REVERT: A 940 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: B 169 LEU cc_start: 0.8209 (mt) cc_final: 0.7997 (mp) REVERT: B 633 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.5619 (t-90) REVERT: B 768 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7917 (ttm110) REVERT: B 1064 ASP cc_start: 0.6595 (t70) cc_final: 0.6211 (t0) REVERT: C 183 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7697 (mmtp) REVERT: C 413 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.4744 (mt) REVERT: C 587 ASN cc_start: 0.6920 (p0) cc_final: 0.6449 (p0) REVERT: C 1156 MET cc_start: 0.2978 (mmm) cc_final: 0.2733 (mpm) REVERT: D 172 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7563 (tp) REVERT: D 235 ASP cc_start: 0.7886 (m-30) cc_final: 0.7505 (m-30) REVERT: D 421 MET cc_start: 0.7506 (tpp) cc_final: 0.7165 (mmm) REVERT: D 918 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7014 (tt0) outliers start: 59 outliers final: 39 residues processed: 414 average time/residue: 1.5639 time to fit residues: 761.1767 Evaluate side-chains 404 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 359 time to evaluate : 3.714 ------------------------------------------------------------------------------- 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 932 LEU 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 227 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 418 MET 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 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 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 688 VAL 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 247 LYS 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 1061 ASP Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 160 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 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 B 531 HIS C 531 HIS D 531 HIS D1135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.160489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126033 restraints weight = 67721.920| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.06 r_work: 0.3235 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32576 Z= 0.120 Angle : 0.540 11.871 44060 Z= 0.277 Chirality : 0.039 0.167 4924 Planarity : 0.005 0.080 5480 Dihedral : 8.062 69.986 4778 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.26 % Allowed : 15.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.14), residues: 3812 helix: 2.06 (0.11), residues: 2456 sheet: 0.03 (0.31), residues: 224 loop : -1.27 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 763 HIS 0.004 0.001 HIS A 151 PHE 0.031 0.001 PHE A1047 TYR 0.013 0.001 TYR D1048 ARG 0.021 0.000 ARG C 768 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 1741) hydrogen bonds : angle 3.40736 ( 5149) covalent geometry : bond 0.00269 (32576) covalent geometry : angle 0.54045 (44060) ********************** 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 417 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 3.692 Fit side-chains revert: symmetry clash REVERT: A 442 LEU cc_start: 0.8435 (mm) cc_final: 0.8138 (mt) REVERT: A 685 ASN cc_start: 0.7012 (m-40) cc_final: 0.6625 (t0) REVERT: A 768 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7910 (ttp-110) REVERT: A 918 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7042 (tt0) REVERT: A 932 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5792 (mm) REVERT: B 169 LEU cc_start: 0.8201 (mt) cc_final: 0.7971 (mp) REVERT: B 633 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5521 (t-90) REVERT: B 768 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7859 (ttm110) REVERT: B 1064 ASP cc_start: 0.6553 (t70) cc_final: 0.6213 (t0) REVERT: C 151 HIS cc_start: 0.6295 (OUTLIER) cc_final: 0.5935 (p90) REVERT: C 183 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7695 (mmtp) REVERT: C 413 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.4714 (mt) REVERT: C 587 ASN cc_start: 0.6925 (p0) cc_final: 0.6440 (p0) REVERT: C 768 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7736 (ttm-80) REVERT: C 1156 MET cc_start: 0.3099 (mmm) cc_final: 0.2864 (mpm) REVERT: D 231 ARG cc_start: 0.7554 (ttp-110) cc_final: 0.7055 (mtp-110) REVERT: D 235 ASP cc_start: 0.7853 (m-30) cc_final: 0.7480 (m-30) REVERT: D 421 MET cc_start: 0.7553 (tpp) cc_final: 0.7216 (mmm) REVERT: D 918 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6973 (tt0) outliers start: 43 outliers final: 31 residues processed: 407 average time/residue: 1.7481 time to fit residues: 832.3608 Evaluate side-chains 399 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 363 time to evaluate : 3.528 ------------------------------------------------------------------------------- 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 932 LEU 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 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 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 1061 ASP Chi-restraints excluded: chain D residue 1191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 323 optimal weight: 0.0870 chunk 22 optimal weight: 0.4980 chunk 166 optimal weight: 7.9990 chunk 268 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 357 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 116 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 151 HIS C 531 HIS D 531 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.161354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126332 restraints weight = 78997.115| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.87 r_work: 0.3208 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32576 Z= 0.110 Angle : 0.528 9.787 44060 Z= 0.271 Chirality : 0.038 0.165 4924 Planarity : 0.005 0.078 5480 Dihedral : 7.904 70.144 4778 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 1.38 % Allowed : 15.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.14), residues: 3812 helix: 2.20 (0.11), residues: 2444 sheet: 0.12 (0.31), residues: 224 loop : -1.22 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 763 HIS 0.004 0.001 HIS C 531 PHE 0.030 0.001 PHE A1047 TYR 0.013 0.001 TYR D1048 ARG 0.019 0.000 ARG C 768 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 1741) hydrogen bonds : angle 3.36819 ( 5149) covalent geometry : bond 0.00231 (32576) covalent geometry : angle 0.52849 (44060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28225.96 seconds wall clock time: 490 minutes 52.06 seconds (29452.06 seconds total)