Starting phenix.real_space_refine on Mon Sep 14 15:14:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.map" model { file = "/net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uv5_20904/09_2026/6uv5_20904.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 181 5.16 5 C 20403 2.51 5 N 5395 2.21 5 O 5960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31954 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 120 Unusual residues: {'ACO': 2, 'OAA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 120 Unusual residues: {'ACO': 2, 'OAA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 69 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'OAA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C AACO A1202 " occ=0.50 ... (100 atoms not shown) pdb=" S1PBACO A1202 " occ=0.50 Time building chain proxies: 12.31, per 1000 atoms: 0.39 Number of scatterers: 31954 At special positions: 0 Unit cell: (140.07, 170.52, 173.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 181 16.00 P 15 15.00 O 5960 8.00 N 5395 7.00 C 20403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 4.3 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 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: 162 helices and 34 sheets defined 45.1% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.772A pdb=" N ILE A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.069A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.747A pdb=" N LEU A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.583A pdb=" N LYS A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.511A pdb=" N ILE A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 312 through 326 removed outlier: 3.651A pdb=" N LEU A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 364 removed outlier: 3.689A pdb=" N THR A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.281A pdb=" N LEU A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 412 through 419 removed outlier: 4.311A pdb=" N GLY A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.738A pdb=" N ALA A 559 " --> pdb=" O ASN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.738A pdb=" N SER A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 664 through 678 removed outlier: 4.089A pdb=" N ASN A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 4.086A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.738A pdb=" N ILE A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 770 removed outlier: 4.004A pdb=" N GLU A 770 " --> pdb=" O GLN A 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 767 through 770' Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 792 through 806 Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.516A pdb=" N ALA A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 877 removed outlier: 3.563A pdb=" N VAL A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 897 removed outlier: 3.861A pdb=" N GLN A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 897 " --> pdb=" O CYS A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 915 Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.508A pdb=" N SER A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 953 removed outlier: 3.528A pdb=" N ALA A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 952 " --> pdb=" O LYS A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 965 removed outlier: 3.879A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.921A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 3.613A pdb=" N ASP A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 4.034A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1055 removed outlier: 3.795A pdb=" N ASP A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1079 removed outlier: 4.298A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 3.619A pdb=" N ILE A1091 " --> pdb=" O TRP A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.615A pdb=" N ILE B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.536A pdb=" N LEU B 44 " --> pdb=" O TRP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.537A pdb=" N SER B 52 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 53' Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.905A pdb=" N PHE B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 6.865A pdb=" N VAL B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.844A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.718A pdb=" N LEU B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.553A pdb=" N SER B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'B' and resid 642 through 649 Processing helix chain 'B' and resid 663 through 678 removed outlier: 3.720A pdb=" N SER B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 707 removed outlier: 3.968A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 733 removed outlier: 3.568A pdb=" N ILE B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 781 Processing helix chain 'B' and resid 792 through 807 Processing helix chain 'B' and resid 824 through 831 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 868 through 877 removed outlier: 3.624A pdb=" N VAL B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 896 removed outlier: 3.792A pdb=" N GLN B 888 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 915 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 937 through 953 removed outlier: 3.727A pdb=" N ALA B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 965 Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.661A pdb=" N LEU B 990 " --> pdb=" O ARG B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1018 removed outlier: 3.675A pdb=" N ASP B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1040 Processing helix chain 'B' and resid 1049 through 1055 removed outlier: 3.837A pdb=" N ASP B1053 " --> pdb=" O ASP B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1079 removed outlier: 4.222A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1091 Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.728A pdb=" N ILE C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 4.169A pdb=" N HIS C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.489A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.838A pdb=" N ILE C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 4.495A pdb=" N ILE C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C 193 " --> pdb=" O PHE C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.510A pdb=" N CYS C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.698A pdb=" N LYS C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 312 through 326 removed outlier: 4.590A pdb=" N LEU C 326 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 364 removed outlier: 4.207A pdb=" N THR C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.038A pdb=" N LEU C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 removed outlier: 3.794A pdb=" N GLY C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 removed outlier: 3.703A pdb=" N GLY C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 556 through 563 removed outlier: 3.610A pdb=" N LYS C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS C 563 " --> pdb=" O ALA C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.539A pdb=" N SER C 581 " --> pdb=" O SER C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'C' and resid 642 through 649 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 696 through 705 removed outlier: 3.661A pdb=" N HIS C 700 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 733 removed outlier: 3.708A pdb=" N ILE C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 770 removed outlier: 3.802A pdb=" N GLU C 770 " --> pdb=" O GLN C 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 767 through 770' Processing helix chain 'C' and resid 771 through 782 removed outlier: 3.593A pdb=" N ALA C 782 " --> pdb=" O ALA C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 805 Processing helix chain 'C' and resid 824 through 831 Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 877 removed outlier: 3.549A pdb=" N VAL C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 897 removed outlier: 3.805A pdb=" N GLN C 888 " --> pdb=" O LYS C 884 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 889 " --> pdb=" O TYR C 885 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 897 " --> pdb=" O CYS C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 916 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 938 through 951 removed outlier: 3.679A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 965 removed outlier: 4.076A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 997 removed outlier: 3.899A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.744A pdb=" N ASP C1005 " --> pdb=" O THR C1001 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C1016 " --> pdb=" O LYS C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1040 removed outlier: 3.543A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS C1040 " --> pdb=" O MET C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1055 removed outlier: 3.909A pdb=" N ASP C1053 " --> pdb=" O ASP C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1079 removed outlier: 4.253A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1091 removed outlier: 3.733A pdb=" N ILE C1091 " --> pdb=" O TRP C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.670A pdb=" N ILE D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 47 Processing helix chain 'D' and resid 48 through 51 Processing helix chain 'D' and resid 65 through 70 Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 225 through 234 removed outlier: 6.517A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.518A pdb=" N ALA D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 312 through 326 removed outlier: 3.690A pdb=" N LEU D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 364 removed outlier: 3.954A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.888A pdb=" N LEU D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 556 through 563 removed outlier: 3.691A pdb=" N HIS D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.666A pdb=" N SER D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 Processing helix chain 'D' and resid 642 through 649 Processing helix chain 'D' and resid 664 through 678 removed outlier: 3.549A pdb=" N ASN D 668 " --> pdb=" O GLY D 664 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 669 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.758A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 733 removed outlier: 3.836A pdb=" N ILE D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 770 Processing helix chain 'D' and resid 771 through 781 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 805 Processing helix chain 'D' and resid 824 through 831 Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 868 through 877 removed outlier: 3.501A pdb=" N VAL D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 897 removed outlier: 3.856A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 897 " --> pdb=" O CYS D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 916 Processing helix chain 'D' and resid 919 through 929 Processing helix chain 'D' and resid 937 through 953 removed outlier: 3.583A pdb=" N ALA D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 966 removed outlier: 3.855A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU D 966 " --> pdb=" O LYS D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 3.747A pdb=" N ASP D1005 " --> pdb=" O THR D1001 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 3.947A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D1039 " --> pdb=" O ASP D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1055 Processing helix chain 'D' and resid 1057 through 1079 removed outlier: 4.280A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1091 removed outlier: 3.659A pdb=" N ILE D1091 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.540A pdb=" N ALA A 218 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 200 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS A 220 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR A 199 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA A 125 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU A 201 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE A 123 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN A 203 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL A 121 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.540A pdb=" N ALA A 218 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 200 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS A 220 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.345A pdb=" N VAL A 57 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL A 74 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.567A pdb=" N LYS A 336 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE A 376 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 338 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ARG A 378 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 340 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 543 removed outlier: 7.171A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 569 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 594 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 630 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 686 removed outlier: 6.827A pdb=" N VAL A 657 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLY A 684 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 659 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA A 686 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 661 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA A 658 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU A 716 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 660 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 713 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TRP A 743 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 715 " --> pdb=" O TRP A 743 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.449A pdb=" N ALA B 218 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 200 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS B 220 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR B 199 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ALA B 125 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLU B 201 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 123 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN B 203 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL B 121 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 129 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.449A pdb=" N ALA B 218 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 200 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS B 220 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.433A pdb=" N VAL B 57 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL B 74 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 93 through 95 Processing sheet with id=AB5, first strand: chain 'B' and resid 263 through 268 Processing sheet with id=AB6, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.346A pdb=" N LYS B 336 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 376 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU B 338 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ARG B 378 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 340 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 537 through 543 removed outlier: 7.219A pdb=" N ALA B 527 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N PHE B 553 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET B 529 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS B 498 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 569 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 500 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN B 571 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP B 502 " --> pdb=" O ASN B 571 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 681 through 686 removed outlier: 7.070A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU B 716 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 660 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.371A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE C 119 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.371A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AC3, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AC4, first strand: chain 'C' and resid 263 through 268 Processing sheet with id=AC5, first strand: chain 'C' and resid 275 through 278 removed outlier: 6.480A pdb=" N LYS C 336 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 376 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 338 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG C 378 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 537 through 543 removed outlier: 7.031A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA C 499 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL C 530 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL C 501 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS C 498 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU C 569 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 500 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN C 571 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP C 502 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP C 567 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA C 595 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 569 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 634 through 635 removed outlier: 6.942A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU C 716 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 660 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLU C 718 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 713 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TRP C 743 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 715 " --> pdb=" O TRP C 743 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE C 745 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY C 717 " --> pdb=" O ILE C 745 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 853 through 854 Processing sheet with id=AC9, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.501A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR D 199 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA D 125 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU D 201 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE D 123 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN D 203 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL D 121 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.501A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 32 through 34 Processing sheet with id=AD3, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AD4, first strand: chain 'D' and resid 263 through 268 Processing sheet with id=AD5, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.575A pdb=" N TRP D 276 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 537 through 543 removed outlier: 7.185A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS D 498 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 568 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE D 594 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 634 through 635 removed outlier: 7.118A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TRP D 743 " --> pdb=" O ILE D 713 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 715 " --> pdb=" O TRP D 743 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE D 745 " --> pdb=" O VAL D 715 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY D 717 " --> pdb=" O ILE D 745 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3864 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: 7.71 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5306 1.29 - 1.43: 8077 1.43 - 1.56: 18924 1.56 - 1.69: 42 1.69 - 1.82: 296 Bond restraints: 32645 Sorted by residual: bond pdb=" C1B ACO A1201 " pdb=" C2B ACO A1201 " ideal model delta sigma weight residual 1.531 1.307 0.224 1.20e-02 6.94e+03 3.48e+02 bond pdb=" C1B ACO B1201 " pdb=" C2B ACO B1201 " ideal model delta sigma weight residual 1.531 1.308 0.223 1.20e-02 6.94e+03 3.45e+02 bond pdb=" C1B ACO D1201 " pdb=" C2B ACO D1201 " ideal model delta sigma weight residual 1.531 1.310 0.221 1.20e-02 6.94e+03 3.40e+02 bond pdb=" C1B ACO D1201 " pdb=" O4B ACO D1201 " ideal model delta sigma weight residual 1.416 1.642 -0.226 1.40e-02 5.10e+03 2.60e+02 bond pdb=" C1B ACO B1201 " pdb=" O4B ACO B1201 " ideal model delta sigma weight residual 1.416 1.640 -0.224 1.40e-02 5.10e+03 2.57e+02 ... (remaining 32640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 43423 3.23 - 6.45: 678 6.45 - 9.68: 108 9.68 - 12.91: 16 12.91 - 16.13: 10 Bond angle restraints: 44235 Sorted by residual: angle pdb=" P1ABACO A1202 " pdb=" O3ABACO A1202 " pdb=" P2ABACO A1202 " ideal model delta sigma weight residual 136.83 120.70 16.13 1.00e+00 1.00e+00 2.60e+02 angle pdb=" P1AAACO A1202 " pdb=" O3AAACO A1202 " pdb=" P2AAACO A1202 " ideal model delta sigma weight residual 136.83 122.22 14.61 1.00e+00 1.00e+00 2.13e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 123.16 13.67 1.00e+00 1.00e+00 1.87e+02 angle pdb=" P1A ACO B1201 " pdb=" O3A ACO B1201 " pdb=" P2A ACO B1201 " ideal model delta sigma weight residual 136.83 123.39 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" N1A ACO B1201 " pdb=" C6A ACO B1201 " pdb=" N6A ACO B1201 " ideal model delta sigma weight residual 118.11 103.13 14.98 1.23e+00 6.64e-01 1.49e+02 ... (remaining 44230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 17910 22.57 - 45.13: 1307 45.13 - 67.70: 138 67.70 - 90.27: 43 90.27 - 112.83: 1 Dihedral angle restraints: 19399 sinusoidal: 7759 harmonic: 11640 Sorted by residual: dihedral pdb=" CA GLY A 967 " pdb=" C GLY A 967 " pdb=" N LYS A 968 " pdb=" CA LYS A 968 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ARG D 835 " pdb=" C ARG D 835 " pdb=" N LYS D 836 " pdb=" CA LYS D 836 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TYR C 854 " pdb=" C TYR C 854 " pdb=" N ALA C 855 " pdb=" CA ALA C 855 " ideal model delta harmonic sigma weight residual -180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 19396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3927 0.073 - 0.147: 870 0.147 - 0.220: 90 0.220 - 0.293: 15 0.293 - 0.367: 15 Chirality restraints: 4917 Sorted by residual: chirality pdb=" CA THR C 842 " pdb=" N THR C 842 " pdb=" C THR C 842 " pdb=" CB THR C 842 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA THR A 842 " pdb=" N THR A 842 " pdb=" C THR A 842 " pdb=" CB THR A 842 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA THR B 842 " pdb=" N THR B 842 " pdb=" C THR B 842 " pdb=" CB THR B 842 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 4914 not shown) Planarity restraints: 5656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7PAACO A1202 " -0.331 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C9PAACO A1202 " 0.077 2.00e-02 2.50e+03 pdb=" CAPAACO A1202 " -0.031 2.00e-02 2.50e+03 pdb=" N8PAACO A1202 " 0.496 2.00e-02 2.50e+03 pdb=" O9PAACO A1202 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3PAACO A1202 " 0.181 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C5PAACO A1202 " -0.039 2.00e-02 2.50e+03 pdb=" C6PAACO A1202 " -0.039 2.00e-02 2.50e+03 pdb=" N4PAACO A1202 " -0.246 2.00e-02 2.50e+03 pdb=" O5PAACO A1202 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 854 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C TYR C 854 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR C 854 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA C 855 " -0.022 2.00e-02 2.50e+03 ... (remaining 5653 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3078 2.74 - 3.28: 30192 3.28 - 3.82: 53302 3.82 - 4.36: 64134 4.36 - 4.90: 110336 Nonbonded interactions: 261042 Sorted by model distance: nonbonded pdb=" CD1 LEU B 833 " pdb=" O HOH B1301 " model vdw 2.199 3.460 nonbonded pdb=" O VAL C 394 " pdb=" OG1 THR C 398 " model vdw 2.234 3.040 nonbonded pdb=" O ALA A 578 " pdb=" OG1 THR A 582 " model vdw 2.249 3.040 nonbonded pdb=" O ALA B 578 " pdb=" OG1 THR B 582 " model vdw 2.261 3.040 nonbonded pdb=" O TRP A 49 " pdb=" OG SER A 52 " model vdw 2.263 3.040 ... (remaining 261037 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 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.050 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 : 0.010 0.226 32645 Z= 0.520 Angle : 1.063 16.134 44235 Z= 0.620 Chirality : 0.063 0.367 4917 Planarity : 0.009 0.285 5656 Dihedral : 15.217 112.833 12007 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.35 % Rotamer: Outliers : 0.50 % Allowed : 7.36 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.10), residues: 4068 helix: -3.08 (0.08), residues: 1726 sheet: -1.62 (0.20), residues: 582 loop : -2.73 (0.12), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG B 848 TYR 0.039 0.003 TYR C 319 PHE 0.024 0.002 PHE A 998 TRP 0.016 0.002 TRP C 84 HIS 0.017 0.002 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00960 / 0.52 (32645) covalent geometry : angle 1.06298 / 0.62 (44235) hydrogen bonds : bond 0.15498 / 10.35 ( 1329) hydrogen bonds : angle 7.86779 / 5.47 ( 3864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 489 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8337 (m-80) cc_final: 0.7770 (m-80) REVERT: A 667 SER cc_start: 0.8008 (p) cc_final: 0.7249 (p) REVERT: A 671 ASN cc_start: 0.8439 (m-40) cc_final: 0.8174 (m-40) REVERT: A 992 ASP cc_start: 0.7624 (m-30) cc_final: 0.7182 (m-30) REVERT: A 1035 ASP cc_start: 0.7711 (t0) cc_final: 0.7425 (t0) REVERT: A 1036 MET cc_start: 0.8486 (tmm) cc_final: 0.8273 (ttp) REVERT: A 1090 ASP cc_start: 0.8238 (t70) cc_final: 0.7811 (t0) REVERT: B 642 MET cc_start: 0.8660 (ttm) cc_final: 0.8416 (ttm) REVERT: B 666 MET cc_start: 0.7481 (mmm) cc_final: 0.7264 (mmt) REVERT: B 965 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8086 (mmtp) REVERT: B 996 GLN cc_start: 0.8367 (mt0) cc_final: 0.8149 (mt0) REVERT: B 1080 LYS cc_start: 0.8733 (mttt) cc_final: 0.8514 (mttm) REVERT: B 1090 ASP cc_start: 0.8360 (t70) cc_final: 0.8068 (t0) REVERT: C 1090 ASP cc_start: 0.8524 (t70) cc_final: 0.8290 (t0) outliers start: 14 outliers final: 7 residues processed: 499 average time/residue: 0.2278 time to fit residues: 178.3152 Evaluate side-chains 360 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 353 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain C residue 620 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 75 ASN A 104 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN A 410 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN A 900 HIS A 908 HIS A 961 ASN A1024 ASN B 27 ASN B 53 GLN B 61 GLN B 299 ASN B 314 GLN B 315 GLN B 638 ASN B 879 GLN B 908 HIS B 961 ASN C 9 GLN C 47 HIS C 270 ASN C 303 ASN C 314 GLN C 645 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN C 879 GLN C 900 HIS C 908 HIS C 909 ASN C 982 ASN C 997 HIS C1024 ASN D 61 GLN D 190 ASN D 203 ASN D 270 ASN D 299 ASN D 403 HIS D 638 ASN D 671 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 HIS D 961 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.187765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155115 restraints weight = 86343.945| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.20 r_work: 0.3542 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (18 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32645 Z= 0.164 Angle : 0.651 9.418 44235 Z= 0.338 Chirality : 0.047 0.192 4917 Planarity : 0.006 0.078 5656 Dihedral : 7.471 107.397 4522 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.40 % Allowed : 11.31 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.12), residues: 4068 helix: -1.43 (0.11), residues: 1770 sheet: -1.42 (0.20), residues: 586 loop : -2.39 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 676 TYR 0.034 0.002 TYR C 319 PHE 0.014 0.001 PHE A 998 TRP 0.010 0.001 TRP B 49 HIS 0.006 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (32645) covalent geometry : angle 0.65141 / 0.34 (44235) hydrogen bonds : bond 0.04168 / 2.80 ( 1329) hydrogen bonds : angle 5.46047 / 3.78 ( 3864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 382 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8987 (tp) cc_final: 0.8618 (tp) REVERT: A 317 TYR cc_start: 0.6973 (t80) cc_final: 0.6764 (t80) REVERT: A 391 MET cc_start: 0.7909 (mmt) cc_final: 0.7676 (mmt) REVERT: A 667 SER cc_start: 0.8332 (p) cc_final: 0.7609 (p) REVERT: A 671 ASN cc_start: 0.8965 (m-40) cc_final: 0.8672 (m-40) REVERT: A 1035 ASP cc_start: 0.8572 (t0) cc_final: 0.8293 (t0) REVERT: A 1090 ASP cc_start: 0.8655 (t70) cc_final: 0.8340 (t0) REVERT: B 835 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8326 (ptm160) REVERT: B 998 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8304 (t80) REVERT: B 1067 MET cc_start: 0.8784 (mtm) cc_final: 0.8554 (mtm) REVERT: B 1090 ASP cc_start: 0.8907 (t70) cc_final: 0.8693 (t0) REVERT: C 1090 ASP cc_start: 0.8769 (t70) cc_final: 0.8559 (t0) outliers start: 43 outliers final: 21 residues processed: 411 average time/residue: 0.2044 time to fit residues: 137.5504 Evaluate side-chains 357 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 334 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 843 SER Chi-restraints excluded: chain D residue 844 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 350 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 175 optimal weight: 0.0030 chunk 182 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 378 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 988 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 168 HIS D 671 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.194831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169019 restraints weight = 89388.695| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.50 r_work: 0.3786 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32645 Z= 0.126 Angle : 0.591 9.520 44235 Z= 0.305 Chirality : 0.045 0.235 4917 Planarity : 0.005 0.073 5656 Dihedral : 6.902 100.203 4513 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.60 % Allowed : 12.77 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.12), residues: 4068 helix: -0.57 (0.12), residues: 1783 sheet: -1.17 (0.21), residues: 574 loop : -2.16 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 676 TYR 0.029 0.001 TYR A 304 PHE 0.024 0.001 PHE A 347 TRP 0.010 0.001 TRP A 84 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (32645) covalent geometry : angle 0.59121 / 0.30 (44235) hydrogen bonds : bond 0.03525 / 2.37 ( 1329) hydrogen bonds : angle 4.91465 / 3.41 ( 3864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 396 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 421 HIS cc_start: 0.6627 (m90) cc_final: 0.6089 (t70) REVERT: A 667 SER cc_start: 0.8213 (p) cc_final: 0.7605 (p) REVERT: A 1035 ASP cc_start: 0.8513 (t0) cc_final: 0.8254 (t0) REVERT: A 1046 GLU cc_start: 0.7608 (tp30) cc_final: 0.7210 (tp30) REVERT: A 1090 ASP cc_start: 0.8540 (t70) cc_final: 0.8232 (t0) REVERT: B 835 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8384 (ptm160) REVERT: B 998 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8183 (t80) REVERT: C 1090 ASP cc_start: 0.8748 (t70) cc_final: 0.8517 (t0) outliers start: 50 outliers final: 28 residues processed: 423 average time/residue: 0.1952 time to fit residues: 133.8210 Evaluate side-chains 383 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 352 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 893 CYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 283 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 292 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 398 optimal weight: 4.9990 chunk 267 optimal weight: 20.0000 chunk 275 optimal weight: 30.0000 chunk 153 optimal weight: 9.9990 chunk 341 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 671 ASN D 672 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.192383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.166645 restraints weight = 87880.836| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.46 r_work: 0.3750 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32645 Z= 0.192 Angle : 0.623 13.502 44235 Z= 0.319 Chirality : 0.047 0.283 4917 Planarity : 0.005 0.075 5656 Dihedral : 6.851 97.721 4513 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.08 % Allowed : 14.31 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.13), residues: 4068 helix: -0.29 (0.12), residues: 1790 sheet: -1.03 (0.21), residues: 574 loop : -2.04 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 676 TYR 0.025 0.002 TYR A 304 PHE 0.028 0.002 PHE A 119 TRP 0.009 0.001 TRP B 49 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (32645) covalent geometry : angle 0.62298 / 0.32 (44235) hydrogen bonds : bond 0.03668 / 2.44 ( 1329) hydrogen bonds : angle 4.86052 / 3.37 ( 3864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7360 (p90) cc_final: 0.7132 (p90) REVERT: A 195 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8634 (tp) REVERT: A 599 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 1001 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7646 (t) REVERT: A 1035 ASP cc_start: 0.8558 (t0) cc_final: 0.8206 (t0) REVERT: A 1046 GLU cc_start: 0.7749 (tp30) cc_final: 0.7496 (tp30) REVERT: A 1090 ASP cc_start: 0.8596 (t70) cc_final: 0.8211 (t0) REVERT: B 504 MET cc_start: 0.8119 (mpp) cc_final: 0.7909 (mmp) REVERT: B 560 MET cc_start: 0.8974 (mmt) cc_final: 0.8720 (mmt) REVERT: B 698 MET cc_start: 0.8289 (mmm) cc_final: 0.7977 (mmm) REVERT: B 919 ASP cc_start: 0.7360 (m-30) cc_final: 0.7098 (m-30) REVERT: B 998 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8223 (t80) REVERT: C 547 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7086 (mm-30) REVERT: D 257 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5731 (t0) outliers start: 66 outliers final: 49 residues processed: 397 average time/residue: 0.1853 time to fit residues: 121.9252 Evaluate side-chains 392 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 893 CYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 126 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 345 optimal weight: 7.9990 chunk 357 optimal weight: 4.9990 chunk 330 optimal weight: 0.2980 chunk 306 optimal weight: 40.0000 chunk 210 optimal weight: 50.0000 chunk 363 optimal weight: 0.1980 chunk 402 optimal weight: 0.7980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 314 GLN C 410 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.193236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166468 restraints weight = 84007.696| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.45 r_work: 0.3763 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32645 Z= 0.154 Angle : 0.598 13.208 44235 Z= 0.306 Chirality : 0.046 0.292 4917 Planarity : 0.004 0.072 5656 Dihedral : 6.714 97.290 4513 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.11 % Allowed : 15.14 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4068 helix: -0.02 (0.12), residues: 1791 sheet: -0.95 (0.21), residues: 576 loop : -1.93 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 676 TYR 0.024 0.001 TYR A 304 PHE 0.024 0.001 PHE A 347 TRP 0.011 0.001 TRP B 49 HIS 0.005 0.001 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (32645) covalent geometry : angle 0.59795 / 0.31 (44235) hydrogen bonds : bond 0.03460 / 2.30 ( 1329) hydrogen bonds : angle 4.73557 / 3.28 ( 3864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 362 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7337 (p90) cc_final: 0.7042 (p90) REVERT: A 195 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 421 HIS cc_start: 0.6695 (m90) cc_final: 0.6116 (t70) REVERT: A 599 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 1001 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7631 (t) REVERT: A 1035 ASP cc_start: 0.8526 (t0) cc_final: 0.8161 (t0) REVERT: A 1046 GLU cc_start: 0.7616 (tp30) cc_final: 0.7254 (tp30) REVERT: A 1090 ASP cc_start: 0.8528 (t70) cc_final: 0.8158 (t0) REVERT: B 560 MET cc_start: 0.8986 (mmt) cc_final: 0.8739 (mmt) REVERT: B 698 MET cc_start: 0.8246 (mmm) cc_final: 0.7974 (mmm) REVERT: B 835 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8216 (ptm160) REVERT: B 904 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8899 (m) REVERT: B 919 ASP cc_start: 0.7235 (m-30) cc_final: 0.6994 (m-30) REVERT: B 998 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8208 (t80) REVERT: C 547 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7100 (mm-30) REVERT: D 257 ASP cc_start: 0.6178 (OUTLIER) cc_final: 0.5957 (t0) outliers start: 67 outliers final: 44 residues processed: 406 average time/residue: 0.1961 time to fit residues: 131.0329 Evaluate side-chains 396 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 346 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 893 CYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 114 optimal weight: 40.0000 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 267 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 981 ASN C 203 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.195966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170837 restraints weight = 86568.549| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.33 r_work: 0.3821 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32645 Z= 0.109 Angle : 0.568 12.399 44235 Z= 0.289 Chirality : 0.045 0.289 4917 Planarity : 0.004 0.067 5656 Dihedral : 6.373 90.580 4513 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.96 % Allowed : 15.88 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 4068 helix: 0.26 (0.13), residues: 1792 sheet: -0.81 (0.22), residues: 576 loop : -1.83 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 676 TYR 0.025 0.001 TYR A 304 PHE 0.021 0.001 PHE A 347 TRP 0.015 0.001 TRP B 49 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (32645) covalent geometry : angle 0.56832 / 0.29 (44235) hydrogen bonds : bond 0.03122 / 2.08 ( 1329) hydrogen bonds : angle 4.52443 / 3.14 ( 3864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 371 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7269 (p90) cc_final: 0.7020 (p90) REVERT: A 195 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8603 (tp) REVERT: A 690 ASP cc_start: 0.7175 (p0) cc_final: 0.6944 (p0) REVERT: A 1001 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7429 (t) REVERT: A 1035 ASP cc_start: 0.8447 (t0) cc_final: 0.8080 (t0) REVERT: A 1046 GLU cc_start: 0.7516 (tp30) cc_final: 0.7201 (tp30) REVERT: A 1090 ASP cc_start: 0.8468 (t70) cc_final: 0.8169 (t0) REVERT: B 835 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8238 (ptm160) REVERT: B 886 SER cc_start: 0.9057 (p) cc_final: 0.8833 (p) REVERT: B 904 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8847 (m) REVERT: D 1067 MET cc_start: 0.8525 (mtm) cc_final: 0.8243 (ttm) outliers start: 62 outliers final: 39 residues processed: 413 average time/residue: 0.2005 time to fit residues: 137.3860 Evaluate side-chains 395 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 381 optimal weight: 0.7980 chunk 342 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 344 optimal weight: 0.0170 chunk 58 optimal weight: 8.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 545 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.195598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170715 restraints weight = 80372.674| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.23 r_work: 0.3832 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32645 Z= 0.117 Angle : 0.570 12.401 44235 Z= 0.289 Chirality : 0.045 0.342 4917 Planarity : 0.004 0.067 5656 Dihedral : 6.192 87.926 4513 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.05 % Allowed : 15.83 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4068 helix: 0.39 (0.13), residues: 1789 sheet: -0.71 (0.22), residues: 574 loop : -1.75 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 507 TYR 0.031 0.001 TYR B 131 PHE 0.021 0.001 PHE A 347 TRP 0.015 0.001 TRP B 49 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (32645) covalent geometry : angle 0.57030 / 0.29 (44235) hydrogen bonds : bond 0.03124 / 2.08 ( 1329) hydrogen bonds : angle 4.49079 / 3.11 ( 3864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 358 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7248 (p90) cc_final: 0.7003 (p90) REVERT: A 195 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8713 (tp) REVERT: A 690 ASP cc_start: 0.7291 (p0) cc_final: 0.7025 (p0) REVERT: A 1001 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7422 (t) REVERT: A 1035 ASP cc_start: 0.8477 (t0) cc_final: 0.8103 (t0) REVERT: A 1046 GLU cc_start: 0.7481 (tp30) cc_final: 0.7217 (tp30) REVERT: A 1090 ASP cc_start: 0.8447 (t70) cc_final: 0.8107 (t0) REVERT: B 835 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8205 (ptm160) REVERT: B 886 SER cc_start: 0.9081 (p) cc_final: 0.8860 (p) REVERT: B 904 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8818 (m) REVERT: B 998 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8053 (t80) REVERT: B 1097 GLU cc_start: 0.6160 (pp20) cc_final: 0.5888 (pm20) REVERT: D 257 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5576 (t0) REVERT: D 1067 MET cc_start: 0.8529 (mtm) cc_final: 0.8181 (ttm) outliers start: 64 outliers final: 45 residues processed: 406 average time/residue: 0.1977 time to fit residues: 133.8432 Evaluate side-chains 399 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 348 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 311 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 283 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 chunk 364 optimal weight: 0.0670 chunk 203 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 overall best weight: 1.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 ASN D 168 HIS ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.193187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.166056 restraints weight = 84076.465| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.52 r_work: 0.3790 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32645 Z= 0.117 Angle : 0.568 12.766 44235 Z= 0.287 Chirality : 0.045 0.350 4917 Planarity : 0.004 0.066 5656 Dihedral : 6.050 86.686 4513 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.08 % Allowed : 15.97 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4068 helix: 0.48 (0.13), residues: 1791 sheet: -0.65 (0.22), residues: 571 loop : -1.70 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 507 TYR 0.024 0.001 TYR A 307 PHE 0.014 0.001 PHE A 119 TRP 0.028 0.001 TRP A 84 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (32645) covalent geometry : angle 0.56750 / 0.29 (44235) hydrogen bonds : bond 0.03076 / 2.05 ( 1329) hydrogen bonds : angle 4.43374 / 3.07 ( 3864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 364 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1001 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7404 (t) REVERT: A 1035 ASP cc_start: 0.8530 (t0) cc_final: 0.8157 (t0) REVERT: A 1046 GLU cc_start: 0.7550 (tp30) cc_final: 0.7287 (tp30) REVERT: A 1090 ASP cc_start: 0.8511 (t70) cc_final: 0.8154 (t0) REVERT: B 835 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8184 (ptm160) REVERT: B 886 SER cc_start: 0.9059 (p) cc_final: 0.8816 (p) REVERT: B 904 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8825 (m) REVERT: B 998 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8133 (t80) REVERT: B 1097 GLU cc_start: 0.6204 (pp20) cc_final: 0.5970 (pm20) REVERT: C 547 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7343 (mm-30) REVERT: D 257 ASP cc_start: 0.6047 (OUTLIER) cc_final: 0.5662 (t0) REVERT: D 268 LEU cc_start: 0.6540 (mm) cc_final: 0.6130 (tp) REVERT: D 1067 MET cc_start: 0.8566 (mtm) cc_final: 0.8235 (ttm) outliers start: 65 outliers final: 47 residues processed: 412 average time/residue: 0.1999 time to fit residues: 136.6672 Evaluate side-chains 399 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 165 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 356 optimal weight: 0.0980 chunk 319 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 407 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 379 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 HIS A 168 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.168740 restraints weight = 104816.865| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.68 r_work: 0.3749 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32645 Z= 0.170 Angle : 0.604 12.941 44235 Z= 0.306 Chirality : 0.047 0.371 4917 Planarity : 0.004 0.068 5656 Dihedral : 6.107 86.324 4511 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.87 % Allowed : 16.27 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4068 helix: 0.42 (0.13), residues: 1795 sheet: -0.63 (0.22), residues: 571 loop : -1.71 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 788 TYR 0.024 0.001 TYR A 307 PHE 0.014 0.001 PHE A 119 TRP 0.026 0.001 TRP A 84 HIS 0.007 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (32645) covalent geometry : angle 0.60443 / 0.31 (44235) hydrogen bonds : bond 0.03308 / 2.20 ( 1329) hydrogen bonds : angle 4.54366 / 3.15 ( 3864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 360 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 HIS cc_start: 0.6668 (m90) cc_final: 0.6160 (t70) REVERT: A 1001 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7563 (t) REVERT: A 1035 ASP cc_start: 0.8577 (t0) cc_final: 0.8209 (t0) REVERT: A 1046 GLU cc_start: 0.7601 (tp30) cc_final: 0.7329 (tp30) REVERT: A 1090 ASP cc_start: 0.8550 (t70) cc_final: 0.8197 (t0) REVERT: B 560 MET cc_start: 0.9009 (mmt) cc_final: 0.8756 (mmt) REVERT: B 698 MET cc_start: 0.8020 (mmm) cc_final: 0.7749 (mmm) REVERT: B 835 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8101 (ptm160) REVERT: B 904 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8861 (m) REVERT: B 998 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8120 (t80) REVERT: C 547 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7363 (mm-30) REVERT: D 1067 MET cc_start: 0.8584 (mtm) cc_final: 0.8274 (ttm) outliers start: 58 outliers final: 50 residues processed: 405 average time/residue: 0.1967 time to fit residues: 132.4903 Evaluate side-chains 408 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 354 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 17 optimal weight: 6.9990 chunk 340 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 115 optimal weight: 20.0000 chunk 346 optimal weight: 5.9990 chunk 335 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 379 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 overall best weight: 2.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.191357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.165651 restraints weight = 97954.254| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.62 r_work: 0.3746 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32645 Z= 0.148 Angle : 0.599 13.606 44235 Z= 0.302 Chirality : 0.046 0.369 4917 Planarity : 0.004 0.068 5656 Dihedral : 6.085 86.060 4511 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.81 % Allowed : 16.36 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 4068 helix: 0.46 (0.13), residues: 1793 sheet: -0.59 (0.22), residues: 571 loop : -1.67 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 788 TYR 0.022 0.001 TYR A 307 PHE 0.013 0.001 PHE A 119 TRP 0.027 0.001 TRP A 84 HIS 0.005 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (32645) covalent geometry : angle 0.59948 / 0.30 (44235) hydrogen bonds : bond 0.03260 / 2.17 ( 1329) hydrogen bonds : angle 4.52415 / 3.13 ( 3864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 357 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1001 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7623 (t) REVERT: A 1035 ASP cc_start: 0.8592 (t0) cc_final: 0.8215 (t0) REVERT: A 1046 GLU cc_start: 0.7623 (tp30) cc_final: 0.7351 (tp30) REVERT: A 1090 ASP cc_start: 0.8548 (t70) cc_final: 0.8179 (t0) REVERT: B 560 MET cc_start: 0.8981 (mmt) cc_final: 0.8707 (mmt) REVERT: B 698 MET cc_start: 0.8023 (mmm) cc_final: 0.7746 (mmm) REVERT: B 835 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8118 (ptm160) REVERT: B 904 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8890 (m) REVERT: B 998 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8232 (t80) REVERT: C 547 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7377 (mm-30) REVERT: D 1067 MET cc_start: 0.8602 (mtm) cc_final: 0.8290 (ttm) outliers start: 56 outliers final: 51 residues processed: 398 average time/residue: 0.1905 time to fit residues: 126.7025 Evaluate side-chains 405 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 712 MET Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 208 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 284 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 332 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 237 optimal weight: 0.0870 chunk 148 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.194457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.169447 restraints weight = 93913.471| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.45 r_work: 0.3789 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32645 Z= 0.137 Angle : 0.595 13.765 44235 Z= 0.300 Chirality : 0.046 0.369 4917 Planarity : 0.004 0.067 5656 Dihedral : 6.025 85.799 4511 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.84 % Allowed : 16.60 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 4068 helix: 0.51 (0.13), residues: 1796 sheet: -0.50 (0.22), residues: 541 loop : -1.64 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 788 TYR 0.022 0.001 TYR A 307 PHE 0.014 0.001 PHE A 119 TRP 0.058 0.001 TRP B 276 HIS 0.005 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (32645) covalent geometry : angle 0.59484 / 0.30 (44235) hydrogen bonds : bond 0.03209 / 2.13 ( 1329) hydrogen bonds : angle 4.50094 / 3.12 ( 3864) =============================================================================== Job complete usr+sys time: 8237.79 seconds wall clock time: 142 minutes 14.09 seconds (8534.09 seconds total)