Starting phenix.real_space_refine on Fri Mar 6 13:34:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uv5_20904/03_2026/6uv5_20904.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uv5_20904/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uv5_20904/03_2026/6uv5_20904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uv5_20904/03_2026/6uv5_20904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uv5_20904/03_2026/6uv5_20904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uv5_20904/03_2026/6uv5_20904.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 12.55, 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: 2.56 Conformation dependent library (CDL) restraints added in 2.5 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: 1.17 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: 6.81 Time building geometry restraints manager: 3.40 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: 18061 22.57 - 45.13: 1349 45.13 - 67.70: 145 67.70 - 90.27: 48 90.27 - 112.83: 1 Dihedral angle restraints: 19604 sinusoidal: 7964 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 19601 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: 0.660 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.680 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 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 : 15.416 112.833 12212 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 covalent geometry : bond 0.00960 (32645) covalent geometry : angle 1.06298 (44235) hydrogen bonds : bond 0.15498 ( 1329) hydrogen bonds : angle 7.86779 ( 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 : 1.145 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: 0.2141 time to fit residues: 166.1587 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 : 0.828 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.187920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155283 restraints weight = 86289.317| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.20 r_work: 0.3542 rms_B_bonded: 4.16 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 = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32645 Z= 0.162 Angle : 0.649 9.732 44235 Z= 0.336 Chirality : 0.046 0.190 4917 Planarity : 0.006 0.078 5656 Dihedral : 8.778 106.753 4727 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.34 % Allowed : 11.58 % Favored : 87.08 % 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: -2.76 (0.12), residues: 4068 helix: -1.39 (0.11), residues: 1776 sheet: -1.38 (0.21), residues: 562 loop : -2.37 (0.13), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 676 TYR 0.035 0.002 TYR A 304 PHE 0.016 0.001 PHE A 998 TRP 0.011 0.001 TRP B 49 HIS 0.006 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00368 (32645) covalent geometry : angle 0.64865 (44235) hydrogen bonds : bond 0.04027 ( 1329) hydrogen bonds : angle 5.37988 ( 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 429 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 388 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8994 (tp) cc_final: 0.8637 (tp) REVERT: A 317 TYR cc_start: 0.6970 (t80) cc_final: 0.6759 (t80) REVERT: A 391 MET cc_start: 0.7935 (mmt) cc_final: 0.7706 (mmt) REVERT: A 667 SER cc_start: 0.8330 (p) cc_final: 0.7610 (p) REVERT: A 671 ASN cc_start: 0.8935 (m-40) cc_final: 0.8648 (m-40) REVERT: A 1035 ASP cc_start: 0.8581 (t0) cc_final: 0.8295 (t0) REVERT: A 1090 ASP cc_start: 0.8649 (t70) cc_final: 0.8305 (t0) REVERT: B 834 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8742 (pt) REVERT: B 835 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8252 (ptm160) REVERT: B 919 ASP cc_start: 0.7429 (m-30) cc_final: 0.7213 (m-30) REVERT: B 998 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8275 (t80) REVERT: B 1067 MET cc_start: 0.8776 (mtm) cc_final: 0.8545 (mtm) REVERT: B 1090 ASP cc_start: 0.8899 (t70) cc_final: 0.8683 (t0) outliers start: 41 outliers final: 20 residues processed: 416 average time/residue: 0.1893 time to fit residues: 128.5888 Evaluate side-chains 363 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 340 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 834 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 350 optimal weight: 3.9990 chunk 113 optimal weight: 40.0000 chunk 175 optimal weight: 0.0470 chunk 182 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 378 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS B 988 GLN B1024 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 HIS D 9 GLN D 168 HIS D 190 ASN D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.195751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170192 restraints weight = 89004.770| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.47 r_work: 0.3813 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32645 Z= 0.111 Angle : 0.577 9.369 44235 Z= 0.298 Chirality : 0.045 0.224 4917 Planarity : 0.005 0.069 5656 Dihedral : 7.901 98.303 4720 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.63 % Allowed : 12.74 % 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: -1.96 (0.12), residues: 4068 helix: -0.51 (0.12), residues: 1784 sheet: -1.13 (0.21), residues: 574 loop : -2.15 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 676 TYR 0.027 0.001 TYR A 304 PHE 0.020 0.001 PHE A 347 TRP 0.011 0.001 TRP A 84 HIS 0.011 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00240 (32645) covalent geometry : angle 0.57688 (44235) hydrogen bonds : bond 0.03410 ( 1329) hydrogen bonds : angle 4.82736 ( 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 456 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 405 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8536 (tp) REVERT: A 421 HIS cc_start: 0.6611 (m90) cc_final: 0.6088 (t70) REVERT: A 667 SER cc_start: 0.8199 (p) cc_final: 0.7779 (p) REVERT: A 1035 ASP cc_start: 0.8454 (t0) cc_final: 0.8202 (t0) REVERT: A 1046 GLU cc_start: 0.7622 (tp30) cc_final: 0.7219 (tp30) REVERT: A 1090 ASP cc_start: 0.8495 (t70) cc_final: 0.8179 (t0) REVERT: B 698 MET cc_start: 0.8154 (mmm) cc_final: 0.7780 (mmm) REVERT: B 835 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8461 (ptm160) REVERT: B 998 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8121 (t80) REVERT: D 194 ASP cc_start: 0.7495 (p0) cc_final: 0.7234 (p0) outliers start: 51 outliers final: 28 residues processed: 430 average time/residue: 0.1960 time to fit residues: 136.6606 Evaluate side-chains 382 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 351 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 B residue 1026 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 666 MET 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 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 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: 4.9990 chunk 151 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 330 optimal weight: 4.9990 chunk 398 optimal weight: 3.9990 chunk 267 optimal weight: 30.0000 chunk 275 optimal weight: 30.0000 chunk 153 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 HIS B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS B1081 GLN C 410 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 HIS C 961 ASN D 168 HIS ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.191928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.165187 restraints weight = 80996.635| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.40 r_work: 0.3751 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32645 Z= 0.216 Angle : 0.638 13.001 44235 Z= 0.327 Chirality : 0.047 0.205 4917 Planarity : 0.005 0.076 5656 Dihedral : 7.866 96.622 4718 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.90 % Allowed : 14.16 % Favored : 83.94 % 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: -0.30 (0.12), residues: 1795 sheet: -0.99 (0.22), residues: 574 loop : -2.04 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 881 TYR 0.023 0.002 TYR A 304 PHE 0.018 0.002 PHE C 998 TRP 0.010 0.001 TRP B 49 HIS 0.008 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00510 (32645) covalent geometry : angle 0.63750 (44235) hydrogen bonds : bond 0.03752 ( 1329) hydrogen bonds : angle 4.86770 ( 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 417 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 357 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7282 (p90) cc_final: 0.7045 (p90) REVERT: A 195 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8734 (tp) REVERT: A 1001 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7646 (t) REVERT: A 1035 ASP cc_start: 0.8550 (t0) cc_final: 0.8194 (t0) REVERT: A 1046 GLU cc_start: 0.7727 (tp30) cc_final: 0.7463 (tp30) REVERT: A 1090 ASP cc_start: 0.8601 (t70) cc_final: 0.8244 (t0) REVERT: B 560 MET cc_start: 0.8972 (mmt) cc_final: 0.8710 (mmt) REVERT: B 698 MET cc_start: 0.8281 (mmm) cc_final: 0.8015 (mmm) REVERT: B 919 ASP cc_start: 0.7460 (m-30) cc_final: 0.7179 (m-30) REVERT: B 998 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8226 (t80) REVERT: C 504 MET cc_start: 0.8624 (mmm) cc_final: 0.8402 (tpp) outliers start: 60 outliers final: 41 residues processed: 397 average time/residue: 0.1870 time to fit residues: 121.8306 Evaluate side-chains 383 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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 62 LEU Chi-restraints excluded: chain D residue 131 TYR 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 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: 1.9990 chunk 142 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 345 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 306 optimal weight: 40.0000 chunk 210 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 402 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** 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 = 0.4335 r_free = 0.4335 target = 0.192263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166622 restraints weight = 76110.821| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.18 r_work: 0.3748 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2239 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= 0.190 Angle : 0.613 11.874 44235 Z= 0.314 Chirality : 0.047 0.280 4917 Planarity : 0.004 0.075 5656 Dihedral : 7.681 94.210 4718 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.02 % Allowed : 14.96 % Favored : 83.02 % 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: -1.48 (0.13), residues: 4068 helix: -0.10 (0.12), residues: 1804 sheet: -0.93 (0.22), residues: 576 loop : -1.94 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 788 TYR 0.023 0.001 TYR A 304 PHE 0.014 0.001 PHE C 998 TRP 0.011 0.001 TRP B 49 HIS 0.010 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00450 (32645) covalent geometry : angle 0.61305 (44235) hydrogen bonds : bond 0.03591 ( 1329) hydrogen bonds : angle 4.78543 ( 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 420 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 356 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8739 (tp) REVERT: A 1001 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7620 (t) REVERT: A 1035 ASP cc_start: 0.8502 (t0) cc_final: 0.8134 (t0) REVERT: A 1046 GLU cc_start: 0.7627 (tp30) cc_final: 0.7195 (tp30) REVERT: A 1090 ASP cc_start: 0.8567 (t70) cc_final: 0.8244 (t0) REVERT: B 183 SER cc_start: 0.8148 (m) cc_final: 0.7939 (t) REVERT: B 560 MET cc_start: 0.8981 (mmt) cc_final: 0.8744 (mmt) REVERT: B 904 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8904 (m) REVERT: B 919 ASP cc_start: 0.7306 (m-30) cc_final: 0.7064 (m-30) REVERT: B 998 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8214 (t80) REVERT: C 504 MET cc_start: 0.8619 (mmm) cc_final: 0.8326 (tpp) REVERT: D 257 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.6088 (t0) outliers start: 64 outliers final: 45 residues processed: 398 average time/residue: 0.1848 time to fit residues: 121.5832 Evaluate side-chains 390 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 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 15 LEU 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 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: 8.9990 chunk 96 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1024 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.190023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.162787 restraints weight = 81468.319| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.44 r_work: 0.3750 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32645 Z= 0.163 Angle : 0.603 12.582 44235 Z= 0.307 Chirality : 0.046 0.295 4917 Planarity : 0.004 0.073 5656 Dihedral : 7.499 90.625 4718 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.17 % Allowed : 15.71 % 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: -1.32 (0.13), residues: 4068 helix: 0.06 (0.12), residues: 1796 sheet: -0.86 (0.22), residues: 574 loop : -1.87 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 788 TYR 0.023 0.001 TYR A 304 PHE 0.024 0.001 PHE A 347 TRP 0.012 0.001 TRP B 49 HIS 0.010 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00385 (32645) covalent geometry : angle 0.60285 (44235) hydrogen bonds : bond 0.03480 ( 1329) hydrogen bonds : angle 4.70455 ( 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 413 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 345 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8699 (tp) REVERT: A 1001 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7614 (t) REVERT: A 1035 ASP cc_start: 0.8549 (t0) cc_final: 0.8189 (t0) REVERT: A 1046 GLU cc_start: 0.7659 (tp30) cc_final: 0.7235 (tp30) REVERT: A 1090 ASP cc_start: 0.8615 (t70) cc_final: 0.8292 (t0) REVERT: B 560 MET cc_start: 0.9005 (mmt) cc_final: 0.8800 (mmt) REVERT: B 904 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8936 (m) REVERT: B 919 ASP cc_start: 0.7457 (m-30) cc_final: 0.7209 (m-30) REVERT: B 998 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8264 (t80) REVERT: C 504 MET cc_start: 0.8660 (mmm) cc_final: 0.8357 (tpp) REVERT: D 257 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.6112 (t0) outliers start: 68 outliers final: 46 residues processed: 392 average time/residue: 0.1806 time to fit residues: 117.2283 Evaluate side-chains 391 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 340 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 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 833 LEU 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 15 LEU 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 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: 0.0770 chunk 342 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 246 optimal weight: 30.0000 chunk 285 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN B 314 GLN B 346 ASN B 403 HIS B 545 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 ASN D 168 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.196342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.171414 restraints weight = 72671.259| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.11 r_work: 0.3845 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- 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 = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32645 Z= 0.105 Angle : 0.563 13.170 44235 Z= 0.288 Chirality : 0.045 0.295 4917 Planarity : 0.004 0.067 5656 Dihedral : 7.090 88.649 4718 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.90 % Allowed : 16.15 % 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: -1.04 (0.13), residues: 4068 helix: 0.33 (0.13), residues: 1794 sheet: -0.73 (0.22), residues: 576 loop : -1.76 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 788 TYR 0.025 0.001 TYR A 304 PHE 0.016 0.001 PHE D 354 TRP 0.028 0.001 TRP A 84 HIS 0.011 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00232 (32645) covalent geometry : angle 0.56344 (44235) hydrogen bonds : bond 0.03097 ( 1329) hydrogen bonds : angle 4.46117 ( 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 427 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 368 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7239 (p90) cc_final: 0.7011 (p90) REVERT: A 195 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8623 (tp) REVERT: A 599 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 985 MET cc_start: 0.8224 (tpp) cc_final: 0.8006 (tpt) REVERT: A 1001 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7399 (t) REVERT: A 1035 ASP cc_start: 0.8424 (t0) cc_final: 0.8049 (t0) REVERT: A 1046 GLU cc_start: 0.7534 (tp30) cc_final: 0.7232 (tp30) REVERT: A 1090 ASP cc_start: 0.8453 (t70) cc_final: 0.8143 (t0) REVERT: B 560 MET cc_start: 0.8914 (mmt) cc_final: 0.8667 (mmt) REVERT: B 698 MET cc_start: 0.8072 (mmm) cc_final: 0.7807 (mmm) REVERT: B 835 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8263 (ptm160) REVERT: B 886 SER cc_start: 0.9017 (p) cc_final: 0.8784 (p) REVERT: B 904 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8867 (m) REVERT: B 998 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8263 (t80) REVERT: C 504 MET cc_start: 0.8653 (mmm) cc_final: 0.8375 (tpp) REVERT: C 547 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7185 (mm-30) REVERT: D 257 ASP cc_start: 0.6042 (OUTLIER) cc_final: 0.5689 (t0) outliers start: 59 outliers final: 42 residues processed: 410 average time/residue: 0.1804 time to fit residues: 122.5659 Evaluate side-chains 394 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 346 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 954 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1001 THR 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 565 GLU 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 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 C residue 940 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: 9.9990 chunk 72 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 283 optimal weight: 0.0570 chunk 210 optimal weight: 0.0050 chunk 364 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 overall best weight: 1.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.195795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.170858 restraints weight = 80868.705| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.23 r_work: 0.3832 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32645 Z= 0.114 Angle : 0.565 13.046 44235 Z= 0.288 Chirality : 0.045 0.347 4917 Planarity : 0.004 0.081 5656 Dihedral : 6.994 87.764 4718 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.75 % Allowed : 16.24 % Favored : 82.01 % 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: -0.89 (0.13), residues: 4068 helix: 0.46 (0.13), residues: 1791 sheet: -0.64 (0.22), residues: 574 loop : -1.69 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 788 TYR 0.023 0.001 TYR A 304 PHE 0.019 0.001 PHE D 790 TRP 0.027 0.001 TRP A 84 HIS 0.011 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00261 (32645) covalent geometry : angle 0.56470 (44235) hydrogen bonds : bond 0.03109 ( 1329) hydrogen bonds : angle 4.41632 ( 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 412 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 358 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7284 (p90) cc_final: 0.7002 (p90) REVERT: A 599 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 985 MET cc_start: 0.8249 (tpp) cc_final: 0.8047 (tpt) REVERT: A 1001 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7393 (t) REVERT: A 1035 ASP cc_start: 0.8479 (t0) cc_final: 0.8106 (t0) REVERT: A 1046 GLU cc_start: 0.7483 (tp30) cc_final: 0.7195 (tp30) REVERT: A 1090 ASP cc_start: 0.8496 (t70) cc_final: 0.8127 (t0) REVERT: B 698 MET cc_start: 0.8089 (mmm) cc_final: 0.7855 (mmm) REVERT: B 835 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8267 (ptm160) REVERT: B 904 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8839 (m) REVERT: B 1097 GLU cc_start: 0.6115 (pp20) cc_final: 0.5819 (pm20) REVERT: C 504 MET cc_start: 0.8676 (mmm) cc_final: 0.8387 (tpp) REVERT: C 547 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 257 ASP cc_start: 0.6065 (OUTLIER) cc_final: 0.5684 (t0) outliers start: 54 outliers final: 43 residues processed: 400 average time/residue: 0.1800 time to fit residues: 120.8418 Evaluate side-chains 387 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 340 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 642 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 VAL 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 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 565 GLU 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 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 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 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 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: 0.9980 chunk 96 optimal weight: 0.8980 chunk 356 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 chunk 407 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 379 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.195034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.170257 restraints weight = 97937.397| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.53 r_work: 0.3791 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32645 Z= 0.133 Angle : 0.585 13.570 44235 Z= 0.296 Chirality : 0.046 0.356 4917 Planarity : 0.004 0.067 5656 Dihedral : 6.991 85.543 4718 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.84 % Allowed : 16.45 % Favored : 81.71 % 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: -0.84 (0.13), residues: 4068 helix: 0.50 (0.13), residues: 1800 sheet: -0.60 (0.22), residues: 576 loop : -1.67 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 881 TYR 0.021 0.001 TYR A 307 PHE 0.013 0.001 PHE A 347 TRP 0.027 0.001 TRP A 84 HIS 0.012 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00311 (32645) covalent geometry : angle 0.58454 (44235) hydrogen bonds : bond 0.03185 ( 1329) hydrogen bonds : angle 4.43778 ( 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 412 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 355 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.7248 (p90) cc_final: 0.6984 (p90) REVERT: A 599 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 1001 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7478 (t) REVERT: A 1035 ASP cc_start: 0.8555 (t0) cc_final: 0.8186 (t0) REVERT: A 1046 GLU cc_start: 0.7525 (tp30) cc_final: 0.7251 (tp30) REVERT: A 1090 ASP cc_start: 0.8563 (t70) cc_final: 0.8196 (t0) REVERT: B 698 MET cc_start: 0.8157 (mmm) cc_final: 0.7903 (mmm) REVERT: B 835 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8227 (ptm160) REVERT: B 904 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8840 (m) REVERT: B 998 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8187 (t80) REVERT: B 1097 GLU cc_start: 0.6216 (pp20) cc_final: 0.5927 (pm20) REVERT: C 504 MET cc_start: 0.8677 (mmm) cc_final: 0.8397 (tpp) REVERT: C 547 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7216 (mm-30) outliers start: 57 outliers final: 48 residues processed: 399 average time/residue: 0.1769 time to fit residues: 117.9300 Evaluate side-chains 400 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 348 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 710 VAL 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 108 GLU 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 565 GLU 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 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 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 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: 30.0000 chunk 340 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 346 optimal weight: 8.9990 chunk 335 optimal weight: 0.0980 chunk 5 optimal weight: 40.0000 chunk 243 optimal weight: 0.0370 chunk 9 optimal weight: 20.0000 chunk 379 optimal weight: 0.2980 chunk 20 optimal weight: 20.0000 overall best weight: 3.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.192870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167490 restraints weight = 91705.267| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.46 r_work: 0.3768 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- 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 = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32645 Z= 0.180 Angle : 0.622 14.336 44235 Z= 0.315 Chirality : 0.047 0.374 4917 Planarity : 0.004 0.069 5656 Dihedral : 7.156 84.257 4718 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.87 % Allowed : 16.54 % Favored : 81.59 % 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: -0.89 (0.13), residues: 4068 helix: 0.41 (0.13), residues: 1801 sheet: -0.55 (0.22), residues: 546 loop : -1.65 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 729 TYR 0.021 0.001 TYR A 307 PHE 0.015 0.001 PHE C 998 TRP 0.030 0.001 TRP B 49 HIS 0.012 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00430 (32645) covalent geometry : angle 0.62157 (44235) hydrogen bonds : bond 0.03446 ( 1329) hydrogen bonds : angle 4.56352 ( 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 411 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 353 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 1001 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 1035 ASP cc_start: 0.8564 (t0) cc_final: 0.8200 (t0) REVERT: A 1046 GLU cc_start: 0.7627 (tp30) cc_final: 0.7334 (tp30) REVERT: A 1090 ASP cc_start: 0.8601 (t70) cc_final: 0.8220 (t0) REVERT: B 560 MET cc_start: 0.9005 (mmt) cc_final: 0.8745 (mmt) REVERT: B 904 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8875 (m) REVERT: B 998 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8310 (t80) REVERT: B 1097 GLU cc_start: 0.6216 (pp20) cc_final: 0.5991 (pm20) REVERT: C 504 MET cc_start: 0.8652 (mmm) cc_final: 0.8337 (tpp) outliers start: 58 outliers final: 50 residues processed: 396 average time/residue: 0.1762 time to fit residues: 116.8332 Evaluate side-chains 401 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 710 VAL 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 108 GLU 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 565 GLU 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 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 940 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 998 PHE 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 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: 0.9980 chunk 243 optimal weight: 9.9990 chunk 284 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 237 optimal weight: 0.3980 chunk 148 optimal weight: 0.4980 chunk 295 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** 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 = 0.4372 r_free = 0.4372 target = 0.195570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.169907 restraints weight = 88645.710| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.46 r_work: 0.3806 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32645 Z= 0.117 Angle : 0.596 16.491 44235 Z= 0.299 Chirality : 0.045 0.361 4917 Planarity : 0.004 0.067 5656 Dihedral : 6.944 79.414 4718 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.81 % Allowed : 16.66 % Favored : 81.53 % 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: -0.75 (0.13), residues: 4068 helix: 0.54 (0.13), residues: 1793 sheet: -0.48 (0.22), residues: 548 loop : -1.60 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 729 TYR 0.022 0.001 TYR C 124 PHE 0.015 0.001 PHE A 347 TRP 0.029 0.001 TRP A 84 HIS 0.011 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00266 (32645) covalent geometry : angle 0.59593 (44235) hydrogen bonds : bond 0.03105 ( 1329) hydrogen bonds : angle 4.43914 ( 3864) =============================================================================== Job complete usr+sys time: 7777.45 seconds wall clock time: 133 minutes 53.53 seconds (8033.53 seconds total)