Starting phenix.real_space_refine on Mon Aug 10 07:33:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9t_45370/08_2026/9c9t_45370_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9t_45370/08_2026/9c9t_45370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9t_45370/08_2026/9c9t_45370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9t_45370/08_2026/9c9t_45370.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9t_45370/08_2026/9c9t_45370_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9t_45370/08_2026/9c9t_45370_neut.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.038 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 306 5.49 5 S 108 5.16 5 C 26188 2.51 5 N 7628 2.21 5 O 8854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43084 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3030 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2997 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "Q" Number of atoms: 5278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5278 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 30, 'TRANS': 628} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3963 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 28, 'TRANS': 496} Chain breaks: 4 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 176 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "Y" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 387 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.53, per 1000 atoms: 0.20 Number of scatterers: 43084 At special positions: 0 Unit cell: (131.93, 177.855, 222.11, 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 108 16.00 P 306 15.00 O 8854 8.00 N 7628 7.00 C 26188 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8902 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 38 sheets defined 50.1% alpha, 9.8% beta 135 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 26 through 30 removed outlier: 4.388A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.798A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.620A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.820A pdb=" N VAL B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.176A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 93 through 105 removed outlier: 3.985A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 127 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.531A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.869A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 63 removed outlier: 4.207A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.069A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F 71 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.925A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 removed outlier: 3.538A pdb=" N LEU G 117 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.713A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.644A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'Q' and resid 709 through 724 removed outlier: 3.533A pdb=" N GLY Q 713 " --> pdb=" O TYR Q 709 " (cutoff:3.500A) Processing helix chain 'Q' and resid 736 through 753 Processing helix chain 'Q' and resid 763 through 778 removed outlier: 4.199A pdb=" N HIS Q 768 " --> pdb=" O ALA Q 764 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN Q 769 " --> pdb=" O SER Q 765 " (cutoff:3.500A) Processing helix chain 'Q' and resid 789 through 800 Processing helix chain 'Q' and resid 819 through 826 Processing helix chain 'Q' and resid 826 through 831 Processing helix chain 'Q' and resid 843 through 847 Processing helix chain 'Q' and resid 851 through 859 Processing helix chain 'Q' and resid 878 through 888 Processing helix chain 'Q' and resid 894 through 901 removed outlier: 3.554A pdb=" N PHE Q 898 " --> pdb=" O SER Q 894 " (cutoff:3.500A) Processing helix chain 'Q' and resid 920 through 924 removed outlier: 3.625A pdb=" N LEU Q 924 " --> pdb=" O GLN Q 920 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 920 through 924' Processing helix chain 'Q' and resid 958 through 970 removed outlier: 4.373A pdb=" N LEU Q 963 " --> pdb=" O ARG Q 959 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR Q 964 " --> pdb=" O GLN Q 960 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN Q 965 " --> pdb=" O ALA Q 961 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS Q 968 " --> pdb=" O TYR Q 964 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1005 through 1013 Processing helix chain 'Q' and resid 1014 through 1017 Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.857A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1145 Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1178 removed outlier: 3.829A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1191 Processing helix chain 'Q' and resid 1192 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.563A pdb=" N CYS Q1205 " --> pdb=" O TYR Q1202 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE Q1206 " --> pdb=" O LEU Q1203 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1202 through 1206' Processing helix chain 'Q' and resid 1227 through 1238 Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1280 through 1284 removed outlier: 3.644A pdb=" N SER Q1283 " --> pdb=" O LYS Q1280 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER Q1284 " --> pdb=" O ASN Q1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1280 through 1284' Processing helix chain 'Q' and resid 1290 through 1297 Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 3.646A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1324 through 1329 removed outlier: 3.705A pdb=" N MET Q1328 " --> pdb=" O MET Q1324 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1330 through 1339 removed outlier: 3.725A pdb=" N TYR Q1334 " --> pdb=" O LEU Q1330 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR Q1337 " --> pdb=" O GLU Q1333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG Q1338 " --> pdb=" O TYR Q1334 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1352 through 1364 removed outlier: 3.584A pdb=" N ASP Q1356 " --> pdb=" O GLU Q1352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL Q1358 " --> pdb=" O ARG Q1354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1397 through 1409 removed outlier: 4.068A pdb=" N ALA Q1408 " --> pdb=" O ALA Q1404 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1446 removed outlier: 3.885A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 34 removed outlier: 3.543A pdb=" N ALA R 33 " --> pdb=" O GLU R 30 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR R 34 " --> pdb=" O GLN R 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 30 through 34' Processing helix chain 'R' and resid 82 through 87 removed outlier: 3.654A pdb=" N ASP R 85 " --> pdb=" O VAL R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 95 removed outlier: 3.733A pdb=" N GLN R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 143 through 158 removed outlier: 3.565A pdb=" N TYR R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 215 through 231 Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.639A pdb=" N TYR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 263 removed outlier: 3.770A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 271 Processing helix chain 'R' and resid 440 through 452 Processing helix chain 'R' and resid 464 through 487 Processing helix chain 'R' and resid 490 through 505 Processing helix chain 'R' and resid 548 through 571 Processing helix chain 'R' and resid 585 through 588 removed outlier: 3.545A pdb=" N ASN R 588 " --> pdb=" O ASP R 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 585 through 588' Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 605 through 610 removed outlier: 3.747A pdb=" N GLN R 609 " --> pdb=" O ASN R 605 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS R 610 " --> pdb=" O ILE R 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 605 through 610' Processing helix chain 'R' and resid 616 through 621 removed outlier: 3.706A pdb=" N VAL R 621 " --> pdb=" O GLU R 617 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 626 removed outlier: 3.862A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 627 through 632 Processing helix chain 'R' and resid 637 through 649 removed outlier: 3.770A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 677 removed outlier: 3.531A pdb=" N ALA R 675 " --> pdb=" O GLY R 672 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL R 677 " --> pdb=" O ASN R 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 672 through 677' Processing helix chain 'R' and resid 679 through 692 Processing helix chain 'R' and resid 708 through 720 Processing helix chain 'R' and resid 722 through 727 removed outlier: 4.239A pdb=" N ARG R 725 " --> pdb=" O GLU R 722 " (cutoff:3.500A) Processing helix chain 'R' and resid 731 through 738 Processing helix chain 'S' and resid 29 through 38 removed outlier: 4.337A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL S 36 " --> pdb=" O PHE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.905A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS S 83 " --> pdb=" O THR S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 150 through 156 removed outlier: 3.907A pdb=" N GLU S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.520A pdb=" N ARG T 55 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.748A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 127 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 219 No H-bonds generated for 'chain 'T' and resid 217 through 219' Processing helix chain 'T' and resid 249 through 255 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.679A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP T 297 " --> pdb=" O ALA T 293 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN T 298 " --> pdb=" O LYS T 294 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 Processing helix chain 'T' and resid 317 through 328 removed outlier: 3.812A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 365 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 418 Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.554A pdb=" N CYS T 422 " --> pdb=" O LEU T 418 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 458 Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 4.170A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 107 removed outlier: 3.799A pdb=" N PHE U 107 " --> pdb=" O SER U 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 104 through 107' Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 Processing helix chain 'U' and resid 206 through 209 Processing helix chain 'U' and resid 241 through 248 Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 266 through 284 removed outlier: 3.938A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.821A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 4.133A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 removed outlier: 3.511A pdb=" N SER U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 444 through 447 removed outlier: 3.552A pdb=" N TYR U 447 " --> pdb=" O GLU U 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 444 through 447' Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.664A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.802A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 127 Processing helix chain 'V' and resid 184 through 192 removed outlier: 4.089A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 216 through 219 removed outlier: 3.625A pdb=" N ALA V 219 " --> pdb=" O ASP V 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 216 through 219' Processing helix chain 'V' and resid 249 through 258 removed outlier: 3.554A pdb=" N ARG V 258 " --> pdb=" O VAL V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 272 removed outlier: 3.534A pdb=" N MET V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.715A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 313 through 316 Processing helix chain 'V' and resid 317 through 328 Processing helix chain 'V' and resid 360 through 365 Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 418 Processing helix chain 'V' and resid 419 through 429 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 93 removed outlier: 4.038A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.228A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.979A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.776A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.739A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.680A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.847A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.730A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 443 removed outlier: 3.631A pdb=" N SER W 436 " --> pdb=" O ASP W 432 " (cutoff:3.500A) Processing helix chain 'W' and resid 444 through 447 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.815A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 97 removed outlier: 3.552A pdb=" N ALA X 89 " --> pdb=" O LYS X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.801A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 127 Processing helix chain 'X' and resid 182 through 192 removed outlier: 3.801A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU X 192 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 270 Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.643A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 removed outlier: 3.640A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 418 removed outlier: 3.502A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 428 Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 removed outlier: 3.522A pdb=" N THR X 458 " --> pdb=" O LYS X 454 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 81 through 93 removed outlier: 3.875A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 266 through 283 removed outlier: 3.865A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA Y 278 " --> pdb=" O ASN Y 274 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 302 through 313 removed outlier: 3.842A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.601A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.783A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE Y 403 " --> pdb=" O SER Y 399 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Y' and resid 444 through 447 Processing helix chain 'Z' and resid 251 through 277 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.257A pdb=" N ARG A 83 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.198A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.897A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.162A pdb=" N ARG E 83 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.249A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 728 through 730 removed outlier: 4.008A pdb=" N THR Q 869 " --> pdb=" O LEU Q 729 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET Q 838 " --> pdb=" O LEU Q 866 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU Q 868 " --> pdb=" O MET Q 838 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU Q 840 " --> pdb=" O LEU Q 868 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU Q 784 " --> pdb=" O VAL Q 817 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 948 through 954 removed outlier: 6.135A pdb=" N VAL Q1389 " --> pdb=" O TYR Q1420 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU Q1422 " --> pdb=" O VAL Q1389 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE Q1391 " --> pdb=" O LEU Q1422 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N VAL Q1424 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE Q1343 " --> pdb=" O LEU Q1371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 6.207A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'X' and resid 163 through 172 removed outlier: 3.842A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 209 through 215 removed outlier: 6.134A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.045A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 14 through 15 removed outlier: 6.262A pdb=" N VAL R 14 " --> pdb=" O GLU R 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 61 through 64 removed outlier: 3.526A pdb=" N PHE R 63 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL R 163 " --> pdb=" O ILE R 729 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.787A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 702 Processing sheet with id=AB7, first strand: chain 'S' and resid 125 through 126 Processing sheet with id=AB8, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB9, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.229A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 129 through 151 removed outlier: 6.342A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE T 163 " --> pdb=" O ASP T 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 175 through 181 current: chain 'T' and resid 209 through 215 removed outlier: 6.583A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AC3, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AC4, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.798A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 125 through 147 removed outlier: 6.761A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE U 160 " --> pdb=" O THR U 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 199 through 204 Processing sheet with id=AC6, first strand: chain 'U' and resid 329 through 331 Processing sheet with id=AC7, first strand: chain 'V' and resid 44 through 45 Processing sheet with id=AC8, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.345A pdb=" N ILE V 75 " --> pdb=" O LEU V 338 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER V 340 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU V 77 " --> pdb=" O SER V 340 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.290A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 175 through 178 current: chain 'V' and resid 207 through 214 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 207 through 214 current: chain 'W' and resid 154 through 161 removed outlier: 3.905A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 198 through 204 current: chain 'Z' and resid 315 through 319 Processing sheet with id=AD1, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AD2, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AD3, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.466A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 329 through 331 Processing sheet with id=AD5, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.305A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 344 through 346 removed outlier: 3.656A pdb=" N THR X 345 " --> pdb=" O SER X 355 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER X 355 " --> pdb=" O THR X 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.655A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD9, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.261A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 125 through 146 removed outlier: 6.623A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AE2, first strand: chain 'Y' and resid 330 through 331 1619 hydrogen bonds defined for protein. 4737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 676 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 14.13 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9412 1.33 - 1.46: 10976 1.46 - 1.58: 23191 1.58 - 1.70: 605 1.70 - 1.83: 191 Bond restraints: 44375 Sorted by residual: bond pdb=" C1' DC J 75 " pdb=" N1 DC J 75 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.45e+01 bond pdb=" C1' DT J 73 " pdb=" N1 DT J 73 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.30e+01 bond pdb=" C1' DT J 68 " pdb=" N1 DT J 68 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" C1' DT J 71 " pdb=" N1 DT J 71 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" C1' DC J 66 " pdb=" N1 DC J 66 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.19e+01 ... (remaining 44370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 60875 4.22 - 8.44: 372 8.44 - 12.66: 45 12.66 - 16.88: 6 16.88 - 21.10: 1 Bond angle restraints: 61299 Sorted by residual: angle pdb=" N ASP W 218 " pdb=" CA ASP W 218 " pdb=" C ASP W 218 " ideal model delta sigma weight residual 110.70 95.86 14.84 1.55e+00 4.16e-01 9.17e+01 angle pdb=" C MET W 215 " pdb=" CA MET W 215 " pdb=" CB MET W 215 " ideal model delta sigma weight residual 116.54 108.88 7.66 1.15e+00 7.56e-01 4.44e+01 angle pdb=" O4' DC I -26 " pdb=" C4' DC I -26 " pdb=" C3' DC I -26 " ideal model delta sigma weight residual 106.00 102.38 3.62 6.00e-01 2.78e+00 3.65e+01 angle pdb=" CA LEU H 48 " pdb=" CB LEU H 48 " pdb=" CG LEU H 48 " ideal model delta sigma weight residual 116.30 137.40 -21.10 3.50e+00 8.16e-02 3.63e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.43 107.03 6.40 1.09e+00 8.42e-01 3.45e+01 ... (remaining 61294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 24073 35.81 - 71.61: 2118 71.61 - 107.42: 77 107.42 - 143.23: 2 143.23 - 179.03: 2 Dihedral angle restraints: 26272 sinusoidal: 12500 harmonic: 13772 Sorted by residual: dihedral pdb=" C ASP W 218 " pdb=" N ASP W 218 " pdb=" CA ASP W 218 " pdb=" CB ASP W 218 " ideal model delta harmonic sigma weight residual -122.60 -106.39 -16.21 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" O2A ADP T1001 " pdb=" O3A ADP T1001 " pdb=" PA ADP T1001 " pdb=" PB ADP T1001 " ideal model delta sinusoidal sigma weight residual -60.00 50.96 -110.96 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" CA LEU X 181 " pdb=" C LEU X 181 " pdb=" N ASP X 182 " pdb=" CA ASP X 182 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 26269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 6873 0.117 - 0.233: 243 0.233 - 0.350: 7 0.350 - 0.466: 2 0.466 - 0.583: 1 Chirality restraints: 7126 Sorted by residual: chirality pdb=" CA ASP W 218 " pdb=" N ASP W 218 " pdb=" C ASP W 218 " pdb=" CB ASP W 218 " both_signs ideal model delta sigma weight residual False 2.51 3.09 -0.58 2.00e-01 2.50e+01 8.49e+00 chirality pdb=" CG LEU S 78 " pdb=" CB LEU S 78 " pdb=" CD1 LEU S 78 " pdb=" CD2 LEU S 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE Q 873 " pdb=" CA ILE Q 873 " pdb=" CG1 ILE Q 873 " pdb=" CG2 ILE Q 873 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 7123 not shown) Planarity restraints: 6810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG W 220 " -0.448 9.50e-02 1.11e+02 2.01e-01 2.47e+01 pdb=" NE ARG W 220 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG W 220 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG W 220 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG W 220 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 105 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C GLN G 105 " -0.063 2.00e-02 2.50e+03 pdb=" O GLN G 105 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY G 106 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG W 208 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ARG W 208 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG W 208 " 0.022 2.00e-02 2.50e+03 pdb=" N SER W 209 " 0.019 2.00e-02 2.50e+03 ... (remaining 6807 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 109 2.43 - 3.05: 22860 3.05 - 3.66: 67741 3.66 - 4.28: 98149 4.28 - 4.90: 157306 Nonbonded interactions: 346165 Sorted by model distance: nonbonded pdb=" CD1 LEU W 185 " pdb=" CE MET W 215 " model vdw 1.811 3.880 nonbonded pdb=" OG SER X 355 " pdb=" O VAL X 359 " model vdw 2.251 3.040 nonbonded pdb=" O GLY B 100 " pdb=" OG SER H 63 " model vdw 2.269 3.040 nonbonded pdb=" N2 DG I 29 " pdb=" O2 DC J -29 " model vdw 2.283 2.496 nonbonded pdb=" O THR W 262 " pdb=" OG1 THR W 262 " model vdw 2.286 3.040 ... (remaining 346160 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'T' and resid 22 through 1001) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 1001)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 1001)) } ncs_group { reference = (chain 'U' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 459 or \ resid 1001)) selection = (chain 'W' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 1001)) \ selection = (chain 'Y' and (resid 18 through 459 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 45.480 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.005 0.082 44376 Z= 0.370 Angle : 0.939 21.098 61299 Z= 0.597 Chirality : 0.052 0.583 7126 Planarity : 0.007 0.201 6810 Dihedral : 22.103 179.032 17370 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 25.79 % Favored : 74.21 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.11), residues: 4702 helix: -1.32 (0.09), residues: 2234 sheet: 0.20 (0.20), residues: 677 loop : -1.55 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG V 191 TYR 0.041 0.002 TYR C 40 PHE 0.047 0.002 PHE D 68 TRP 0.035 0.003 TRP Q 854 HIS 0.007 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.37 (44375) covalent geometry : angle 0.93905 / 0.60 (61299) hydrogen bonds : bond 0.14682 / 10.00 ( 1963) hydrogen bonds : angle 5.94359 / 4.17 ( 5413) Misc. bond : bond 0.00170 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 733 MET cc_start: 0.2780 (tpt) cc_final: 0.2477 (tpt) REVERT: T 268 MET cc_start: 0.9058 (mpp) cc_final: 0.8588 (mpp) REVERT: U 185 LEU cc_start: 0.8941 (mm) cc_final: 0.8669 (tt) REVERT: U 322 MET cc_start: 0.9308 (mtm) cc_final: 0.9094 (mtp) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2789 time to fit residues: 120.8683 Evaluate side-chains 235 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Q 808 ASN Q 875 ASN Q1204 ASN Q1362 GLN Q1382 ASN R 144 GLN R 149 ASN R 745 HIS V 427 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.075948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048062 restraints weight = 191368.105| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.27 r_work: 0.2809 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44376 Z= 0.202 Angle : 0.647 12.657 61299 Z= 0.345 Chirality : 0.044 0.262 7126 Planarity : 0.004 0.048 6810 Dihedral : 22.729 179.193 8407 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.63 % Allowed : 23.78 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 4702 helix: 0.27 (0.11), residues: 2284 sheet: 0.31 (0.20), residues: 672 loop : -1.37 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 102 TYR 0.030 0.001 TYR X 462 PHE 0.023 0.001 PHE Q1007 TRP 0.018 0.001 TRP Q 854 HIS 0.004 0.001 HIS Q 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (44375) covalent geometry : angle 0.64744 / 0.35 (61299) hydrogen bonds : bond 0.05278 / 3.41 ( 1963) hydrogen bonds : angle 4.10214 / 2.88 ( 5413) Misc. bond : bond 0.00330 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 234 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8881 (pp20) REVERT: F 64 GLU cc_start: 0.9547 (tt0) cc_final: 0.9278 (mt-10) REVERT: H 59 GLN cc_start: 0.9239 (mp10) cc_final: 0.8965 (pm20) REVERT: Q 733 MET cc_start: 0.3283 (tpt) cc_final: 0.2888 (tpt) REVERT: U 153 HIS cc_start: 0.8062 (t-90) cc_final: 0.7849 (p-80) REVERT: U 276 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9082 (ttmm) REVERT: V 171 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9081 (ttpt) REVERT: Y 279 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8974 (tp30) outliers start: 65 outliers final: 30 residues processed: 277 average time/residue: 0.2709 time to fit residues: 123.8493 Evaluate side-chains 249 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain Q residue 826 ASP Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1324 MET Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 107 optimal weight: 0.9990 chunk 420 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 454 optimal weight: 0.0050 chunk 31 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.076514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.049008 restraints weight = 190396.805| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.42 r_work: 0.2822 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44376 Z= 0.124 Angle : 0.576 12.748 61299 Z= 0.308 Chirality : 0.042 0.274 7126 Planarity : 0.003 0.045 6810 Dihedral : 22.602 178.860 8407 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 23.71 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 4702 helix: 0.92 (0.11), residues: 2286 sheet: 0.47 (0.20), residues: 670 loop : -1.23 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 37 TYR 0.022 0.001 TYR X 462 PHE 0.021 0.001 PHE R 691 TRP 0.016 0.001 TRP Q 854 HIS 0.003 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (44375) covalent geometry : angle 0.57555 / 0.31 (61299) hydrogen bonds : bond 0.04402 / 2.83 ( 1963) hydrogen bonds : angle 3.76238 / 2.64 ( 5413) Misc. bond : bond 0.00181 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 236 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.9517 (mmm-85) cc_final: 0.9066 (ptp-110) REVERT: D 74 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8873 (pp20) REVERT: G 65 GLU cc_start: 0.9137 (tp30) cc_final: 0.8925 (tp30) REVERT: H 59 GLN cc_start: 0.9241 (mp10) cc_final: 0.8990 (pm20) REVERT: H 112 HIS cc_start: 0.9277 (m90) cc_final: 0.8978 (m90) REVERT: H 123 LYS cc_start: 0.9500 (tttp) cc_final: 0.9202 (tmtt) REVERT: Q 733 MET cc_start: 0.3333 (tpt) cc_final: 0.2865 (tpt) REVERT: Q 822 MET cc_start: 0.7976 (tpp) cc_final: 0.7638 (tpp) REVERT: Q 838 MET cc_start: 0.0713 (ptt) cc_final: -0.0449 (mtt) REVERT: R 149 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8487 (t0) REVERT: R 157 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8901 (p) REVERT: U 153 HIS cc_start: 0.8077 (t-90) cc_final: 0.7834 (p-80) REVERT: U 272 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8702 (mt0) REVERT: V 171 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9047 (ttpt) REVERT: V 282 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8398 (tm-30) REVERT: W 182 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8924 (pp20) REVERT: X 312 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: X 444 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9204 (tt) REVERT: Y 86 MET cc_start: 0.8997 (tpp) cc_final: 0.8654 (tpp) REVERT: Y 279 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8851 (tp30) outliers start: 81 outliers final: 35 residues processed: 298 average time/residue: 0.2748 time to fit residues: 135.4782 Evaluate side-chains 261 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1308 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1324 MET Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 272 GLN Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 279 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 168 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 88 optimal weight: 50.0000 chunk 118 optimal weight: 20.0000 chunk 464 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 392 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 79 optimal weight: 50.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1359 HIS ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.075545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047536 restraints weight = 192109.175| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.24 r_work: 0.2795 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 44376 Z= 0.191 Angle : 0.598 12.453 61299 Z= 0.317 Chirality : 0.043 0.271 7126 Planarity : 0.004 0.040 6810 Dihedral : 22.587 178.393 8407 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.56 % Allowed : 23.55 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 4702 helix: 1.29 (0.11), residues: 2266 sheet: 0.49 (0.20), residues: 666 loop : -1.18 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 36 TYR 0.029 0.001 TYR X 462 PHE 0.018 0.001 PHE R 691 TRP 0.019 0.002 TRP Q 854 HIS 0.003 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (44375) covalent geometry : angle 0.59815 / 0.32 (61299) hydrogen bonds : bond 0.04627 / 3.02 ( 1963) hydrogen bonds : angle 3.71483 / 2.61 ( 5413) Misc. bond : bond 0.00396 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 222 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.9506 (mmm-85) cc_final: 0.9131 (mtp85) REVERT: D 74 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8894 (pp20) REVERT: F 60 LYS cc_start: 0.9304 (tptt) cc_final: 0.9076 (tptt) REVERT: F 64 GLU cc_start: 0.9588 (tt0) cc_final: 0.9362 (mt-10) REVERT: F 85 MET cc_start: 0.8692 (ppp) cc_final: 0.8488 (ppp) REVERT: H 59 GLN cc_start: 0.9265 (mp10) cc_final: 0.9023 (pm20) REVERT: Q 838 MET cc_start: 0.0774 (ptt) cc_final: -0.0331 (mtt) REVERT: R 149 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8514 (t0) REVERT: R 157 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8993 (p) REVERT: R 749 ASN cc_start: 0.9488 (OUTLIER) cc_final: 0.8725 (m-40) REVERT: T 191 ARG cc_start: 0.9093 (tmm-80) cc_final: 0.8366 (tmm-80) REVERT: T 271 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7644 (tm-30) REVERT: T 312 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: U 153 HIS cc_start: 0.8065 (t-90) cc_final: 0.7834 (p-80) REVERT: U 276 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9045 (ttmm) REVERT: V 171 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9092 (ttpt) REVERT: V 282 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8473 (tm-30) REVERT: W 182 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8899 (pp20) REVERT: X 312 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: X 444 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9216 (tt) REVERT: Y 86 MET cc_start: 0.9014 (tpp) cc_final: 0.8735 (tpp) REVERT: Y 104 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.9270 (t) REVERT: Y 279 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8884 (tp30) outliers start: 102 outliers final: 58 residues processed: 306 average time/residue: 0.2705 time to fit residues: 137.8559 Evaluate side-chains 278 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1308 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 450 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 431 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 442 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 446 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN F 76 HIS R 132 ASN ** R 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.075536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047927 restraints weight = 191624.386| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.28 r_work: 0.2788 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44376 Z= 0.169 Angle : 0.584 14.390 61299 Z= 0.309 Chirality : 0.042 0.274 7126 Planarity : 0.003 0.039 6810 Dihedral : 22.530 177.808 8407 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 2.74 % Allowed : 23.53 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4702 helix: 1.47 (0.11), residues: 2263 sheet: 0.42 (0.20), residues: 668 loop : -1.11 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 36 TYR 0.026 0.001 TYR X 462 PHE 0.018 0.001 PHE R 691 TRP 0.038 0.002 TRP Q1396 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (44375) covalent geometry : angle 0.58378 / 0.31 (61299) hydrogen bonds : bond 0.04352 / 2.83 ( 1963) hydrogen bonds : angle 3.63651 / 2.56 ( 5413) Misc. bond : bond 0.00512 / 0.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 224 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.9518 (mmm-85) cc_final: 0.9142 (mtp85) REVERT: C 57 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: D 74 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8901 (pp20) REVERT: F 64 GLU cc_start: 0.9580 (tt0) cc_final: 0.9368 (mt-10) REVERT: F 85 MET cc_start: 0.8662 (ppp) cc_final: 0.8449 (ppp) REVERT: G 105 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7032 (tm-30) REVERT: H 59 GLN cc_start: 0.9286 (mp10) cc_final: 0.9023 (pm20) REVERT: H 123 LYS cc_start: 0.9409 (tttp) cc_final: 0.9081 (tmtt) REVERT: Q 781 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6431 (m-80) REVERT: Q 838 MET cc_start: 0.0851 (ptt) cc_final: -0.0248 (mtt) REVERT: R 149 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8543 (t0) REVERT: R 157 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.9050 (p) REVERT: R 749 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.8782 (m-40) REVERT: T 191 ARG cc_start: 0.9118 (tmm-80) cc_final: 0.8456 (tmm-80) REVERT: T 271 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7762 (tm-30) REVERT: T 312 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: U 153 HIS cc_start: 0.8091 (t-90) cc_final: 0.7865 (p-80) REVERT: U 243 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: U 276 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9034 (ttmm) REVERT: U 363 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: V 171 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9080 (ttpt) REVERT: V 282 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8508 (tm-30) REVERT: V 324 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9314 (tt) REVERT: W 182 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8463 (pp20) REVERT: X 312 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: X 444 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9235 (tt) REVERT: Y 86 MET cc_start: 0.9053 (tpp) cc_final: 0.8761 (tpp) REVERT: Y 104 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.9279 (t) REVERT: Y 279 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.8886 (tp30) outliers start: 109 outliers final: 62 residues processed: 317 average time/residue: 0.2639 time to fit residues: 138.3533 Evaluate side-chains 292 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 214 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 781 PHE Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 363 GLU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 388 THR Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 450 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 117 optimal weight: 30.0000 chunk 227 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 90 optimal weight: 50.0000 chunk 12 optimal weight: 6.9990 chunk 302 optimal weight: 0.1980 chunk 301 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.074482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045687 restraints weight = 192343.387| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.08 r_work: 0.2774 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 44376 Z= 0.238 Angle : 0.636 12.728 61299 Z= 0.332 Chirality : 0.043 0.279 7126 Planarity : 0.004 0.043 6810 Dihedral : 22.566 178.503 8407 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 3.04 % Allowed : 23.20 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 4702 helix: 1.53 (0.11), residues: 2270 sheet: 0.37 (0.20), residues: 661 loop : -1.13 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.033 0.001 TYR X 462 PHE 0.017 0.001 PHE R 691 TRP 0.021 0.002 TRP Q1396 HIS 0.014 0.001 HIS H 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (44375) covalent geometry : angle 0.63592 / 0.33 (61299) hydrogen bonds : bond 0.04927 / 3.25 ( 1963) hydrogen bonds : angle 3.75759 / 2.65 ( 5413) Misc. bond : bond 0.00526 / 0.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 217 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.9694 (mm) cc_final: 0.9298 (tp) REVERT: C 57 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8023 (tp30) REVERT: D 74 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8926 (pp20) REVERT: E 82 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9189 (tp) REVERT: F 60 LYS cc_start: 0.9394 (tptt) cc_final: 0.9172 (tptt) REVERT: F 64 GLU cc_start: 0.9594 (tt0) cc_final: 0.9379 (mt-10) REVERT: F 67 ILE cc_start: 0.8714 (tp) cc_final: 0.8230 (tt) REVERT: F 85 MET cc_start: 0.8652 (ppp) cc_final: 0.8414 (ppp) REVERT: H 59 GLN cc_start: 0.9311 (mp10) cc_final: 0.9109 (pm20) REVERT: H 112 HIS cc_start: 0.9253 (m90) cc_final: 0.8965 (m90) REVERT: Q 833 MET cc_start: 0.5386 (mmp) cc_final: 0.5112 (mmp) REVERT: Q 838 MET cc_start: 0.0801 (ptt) cc_final: -0.0228 (mtt) REVERT: R 149 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8528 (t0) REVERT: R 157 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9064 (p) REVERT: R 687 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: R 749 ASN cc_start: 0.9502 (OUTLIER) cc_final: 0.8798 (m-40) REVERT: T 191 ARG cc_start: 0.9112 (tmm-80) cc_final: 0.8465 (tmm-80) REVERT: T 312 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: U 175 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8148 (mmp) REVERT: U 243 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: U 276 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9033 (ttmm) REVERT: U 363 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: V 282 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8523 (tm-30) REVERT: V 324 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9302 (tt) REVERT: W 182 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8445 (pp20) REVERT: X 312 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: Y 86 MET cc_start: 0.9071 (tpp) cc_final: 0.8857 (tpp) REVERT: Y 104 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.9301 (t) REVERT: Y 279 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8910 (tp30) outliers start: 121 outliers final: 76 residues processed: 321 average time/residue: 0.2486 time to fit residues: 131.4720 Evaluate side-chains 302 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 210 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1017 PHE Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 660 THR Chi-restraints excluded: chain R residue 687 GLU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 247 ILE Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 363 GLU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 388 THR Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 450 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 152 optimal weight: 4.9990 chunk 446 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 425 optimal weight: 0.5980 chunk 299 optimal weight: 0.9980 chunk 391 optimal weight: 6.9990 chunk 453 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN F 65 ASN S 162 ASN W 23 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.075731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048142 restraints weight = 190175.429| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.20 r_work: 0.2809 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 44376 Z= 0.115 Angle : 0.573 14.874 61299 Z= 0.302 Chirality : 0.042 0.277 7126 Planarity : 0.003 0.046 6810 Dihedral : 22.447 177.343 8407 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 1.89 % Allowed : 24.53 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.13), residues: 4702 helix: 1.65 (0.11), residues: 2266 sheet: 0.43 (0.20), residues: 660 loop : -1.04 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 68 TYR 0.018 0.001 TYR X 462 PHE 0.017 0.001 PHE R 691 TRP 0.019 0.002 TRP Q1396 HIS 0.007 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (44375) covalent geometry : angle 0.57289 / 0.30 (61299) hydrogen bonds : bond 0.03890 / 2.49 ( 1963) hydrogen bonds : angle 3.49899 / 2.45 ( 5413) Misc. bond : bond 0.00374 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 225 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.9698 (mm) cc_final: 0.9289 (tp) REVERT: B 96 ARG cc_start: 0.9484 (mmm-85) cc_final: 0.8920 (mtp85) REVERT: C 57 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: D 74 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8917 (pp20) REVERT: F 75 GLU cc_start: 0.9202 (pp20) cc_final: 0.8967 (pp20) REVERT: F 85 MET cc_start: 0.8615 (ppp) cc_final: 0.8367 (ppp) REVERT: G 105 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7130 (tm-30) REVERT: H 59 GLN cc_start: 0.9294 (mp10) cc_final: 0.9088 (pm20) REVERT: Q 833 MET cc_start: 0.5594 (mmp) cc_final: 0.5393 (mmp) REVERT: Q 838 MET cc_start: 0.0878 (ptt) cc_final: -0.0142 (mtt) REVERT: R 149 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8558 (t0) REVERT: R 687 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8822 (mt-10) REVERT: R 749 ASN cc_start: 0.9510 (OUTLIER) cc_final: 0.8792 (m-40) REVERT: T 191 ARG cc_start: 0.9133 (tmm-80) cc_final: 0.8865 (tmm-80) REVERT: T 312 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: U 276 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8997 (ttmm) REVERT: V 268 MET cc_start: 0.8863 (mtt) cc_final: 0.8642 (mtt) REVERT: V 282 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8464 (tm-30) REVERT: V 324 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9328 (tt) REVERT: W 182 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8507 (pp20) REVERT: X 312 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: Y 86 MET cc_start: 0.9062 (tpp) cc_final: 0.8787 (tpp) REVERT: Y 166 GLU cc_start: 0.8371 (tp30) cc_final: 0.8033 (tp30) REVERT: Y 279 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8862 (tp30) outliers start: 75 outliers final: 48 residues processed: 284 average time/residue: 0.2690 time to fit residues: 127.1353 Evaluate side-chains 270 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 687 GLU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 279 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 195 optimal weight: 40.0000 chunk 273 optimal weight: 4.9990 chunk 385 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 451 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 421 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 479 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.074862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047501 restraints weight = 192315.666| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.16 r_work: 0.2784 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 44376 Z= 0.190 Angle : 0.607 13.349 61299 Z= 0.317 Chirality : 0.042 0.272 7126 Planarity : 0.003 0.043 6810 Dihedral : 22.432 178.145 8407 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 2.59 % Allowed : 23.98 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.13), residues: 4702 helix: 1.69 (0.11), residues: 2269 sheet: 0.40 (0.20), residues: 661 loop : -1.05 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 102 TYR 0.047 0.001 TYR H 86 PHE 0.017 0.001 PHE R 691 TRP 0.018 0.002 TRP Q1396 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (44375) covalent geometry : angle 0.60715 / 0.32 (61299) hydrogen bonds : bond 0.04446 / 2.91 ( 1963) hydrogen bonds : angle 3.59548 / 2.53 ( 5413) Misc. bond : bond 0.00482 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 217 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.9704 (mm) cc_final: 0.9277 (tp) REVERT: B 96 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.8941 (mtp85) REVERT: C 57 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: D 74 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8927 (pp20) REVERT: F 68 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8656 (mmp80) REVERT: F 85 MET cc_start: 0.8614 (ppp) cc_final: 0.8378 (ppp) REVERT: G 105 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7458 (tm-30) REVERT: H 59 GLN cc_start: 0.9302 (mp10) cc_final: 0.9098 (pm20) REVERT: Q 838 MET cc_start: 0.1066 (ptt) cc_final: -0.0022 (mtt) REVERT: R 149 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8535 (t0) REVERT: R 687 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8801 (mt-10) REVERT: R 749 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.8777 (m-40) REVERT: T 191 ARG cc_start: 0.9143 (tmm-80) cc_final: 0.8877 (tmm-80) REVERT: T 312 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: U 243 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: U 276 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9004 (ttmm) REVERT: V 324 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9319 (tt) REVERT: W 182 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8835 (pp20) REVERT: X 312 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: Y 86 MET cc_start: 0.9110 (tpp) cc_final: 0.8904 (tpp) REVERT: Y 104 SER cc_start: 0.9503 (OUTLIER) cc_final: 0.9264 (t) REVERT: Y 166 GLU cc_start: 0.8371 (tp30) cc_final: 0.8018 (tp30) REVERT: Y 279 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8874 (tp30) outliers start: 103 outliers final: 70 residues processed: 302 average time/residue: 0.2392 time to fit residues: 119.8005 Evaluate side-chains 289 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 207 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1017 PHE Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 660 THR Chi-restraints excluded: chain R residue 687 GLU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 345 THR Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 233 optimal weight: 5.9990 chunk 393 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 312 optimal weight: 2.9990 chunk 369 optimal weight: 7.9990 chunk 355 optimal weight: 3.9990 chunk 196 optimal weight: 40.0000 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Q1180 ASN T 271 GLN ** V 165 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 = 0.3812 r_free = 0.3812 target = 0.074432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047107 restraints weight = 190551.191| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.16 r_work: 0.2775 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 44376 Z= 0.202 Angle : 0.625 15.789 61299 Z= 0.325 Chirality : 0.043 0.272 7126 Planarity : 0.004 0.045 6810 Dihedral : 22.468 177.323 8407 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.64 % Allowed : 23.96 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.13), residues: 4702 helix: 1.66 (0.11), residues: 2269 sheet: 0.29 (0.20), residues: 664 loop : -1.07 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 68 TYR 0.031 0.001 TYR H 86 PHE 0.016 0.001 PHE R 691 TRP 0.022 0.002 TRP Q1396 HIS 0.013 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (44375) covalent geometry : angle 0.62468 / 0.32 (61299) hydrogen bonds : bond 0.04516 / 2.97 ( 1963) hydrogen bonds : angle 3.66081 / 2.58 ( 5413) Misc. bond : bond 0.00480 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 214 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.9707 (mm) cc_final: 0.9286 (tp) REVERT: B 96 ARG cc_start: 0.9480 (mmm-85) cc_final: 0.8943 (mtp85) REVERT: C 57 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: D 74 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8940 (pp20) REVERT: F 68 ARG cc_start: 0.9088 (mmm160) cc_final: 0.8863 (mmp80) REVERT: F 75 GLU cc_start: 0.9249 (pp20) cc_final: 0.9041 (pp20) REVERT: G 105 GLN cc_start: 0.7706 (tm-30) cc_final: 0.6903 (tm-30) REVERT: H 112 HIS cc_start: 0.9250 (m90) cc_final: 0.9009 (m90) REVERT: R 149 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8543 (t0) REVERT: R 157 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9092 (p) REVERT: R 687 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8815 (mt-10) REVERT: T 191 ARG cc_start: 0.9143 (tmm-80) cc_final: 0.8874 (tmm-80) REVERT: T 312 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: U 23 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8563 (p90) REVERT: U 175 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8139 (mmp) REVERT: U 243 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: V 268 MET cc_start: 0.8921 (mtt) cc_final: 0.8671 (mtt) REVERT: V 324 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9316 (tt) REVERT: W 182 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8451 (pp20) REVERT: X 312 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: X 373 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9092 (mm) REVERT: Y 104 SER cc_start: 0.9496 (OUTLIER) cc_final: 0.9285 (t) REVERT: Y 166 GLU cc_start: 0.8387 (tp30) cc_final: 0.8020 (tp30) REVERT: Y 279 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8909 (tp30) outliers start: 105 outliers final: 80 residues processed: 300 average time/residue: 0.2395 time to fit residues: 120.2164 Evaluate side-chains 299 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 205 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1017 PHE Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 660 THR Chi-restraints excluded: chain R residue 687 GLU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 345 THR Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 416 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 89 optimal weight: 50.0000 chunk 365 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 434 optimal weight: 0.7980 chunk 435 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 466 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 414 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.074722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.046983 restraints weight = 192235.676| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.40 r_work: 0.2755 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 44376 Z= 0.163 Angle : 0.611 15.785 61299 Z= 0.317 Chirality : 0.042 0.341 7126 Planarity : 0.003 0.045 6810 Dihedral : 22.428 177.402 8407 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.21 % Allowed : 24.51 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.13), residues: 4702 helix: 1.71 (0.11), residues: 2269 sheet: 0.37 (0.20), residues: 659 loop : -1.03 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 102 TYR 0.031 0.001 TYR H 86 PHE 0.017 0.001 PHE R 691 TRP 0.022 0.002 TRP Q1396 HIS 0.004 0.001 HIS S 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (44375) covalent geometry : angle 0.61131 / 0.32 (61299) hydrogen bonds : bond 0.04278 / 2.79 ( 1963) hydrogen bonds : angle 3.60082 / 2.54 ( 5413) Misc. bond : bond 0.00438 / 0.29 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 207 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.9701 (mm) cc_final: 0.9280 (tp) REVERT: B 96 ARG cc_start: 0.9498 (mmm-85) cc_final: 0.8940 (mtp85) REVERT: C 57 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: D 74 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8927 (pp20) REVERT: F 67 ILE cc_start: 0.8274 (mm) cc_final: 0.7960 (tt) REVERT: F 75 GLU cc_start: 0.9265 (pp20) cc_final: 0.9055 (pp20) REVERT: G 105 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7104 (tm-30) REVERT: Q 838 MET cc_start: 0.1359 (ptt) cc_final: 0.0249 (mtt) REVERT: R 149 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8532 (t0) REVERT: R 157 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9099 (p) REVERT: R 687 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8848 (mt-10) REVERT: T 191 ARG cc_start: 0.9140 (tmm-80) cc_final: 0.8866 (tmm-80) REVERT: T 312 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: U 23 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.8509 (p90) REVERT: U 175 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8043 (mmp) REVERT: U 243 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: U 276 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8970 (ttmm) REVERT: V 324 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9300 (tt) REVERT: W 182 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8466 (pp20) REVERT: X 312 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: X 373 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9082 (mm) REVERT: Y 86 MET cc_start: 0.8989 (tpp) cc_final: 0.8632 (tpp) REVERT: Y 104 SER cc_start: 0.9500 (OUTLIER) cc_final: 0.9286 (t) REVERT: Y 166 GLU cc_start: 0.8390 (tp30) cc_final: 0.8016 (tp30) REVERT: Y 279 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.8916 (tp30) outliers start: 88 outliers final: 71 residues processed: 282 average time/residue: 0.2184 time to fit residues: 103.8466 Evaluate side-chains 288 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 202 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1017 PHE Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 660 THR Chi-restraints excluded: chain R residue 687 GLU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 345 THR Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 416 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 441 optimal weight: 0.5980 chunk 400 optimal weight: 0.8980 chunk 397 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 331 optimal weight: 0.0370 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1180 ASN T 271 GLN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.075071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.047059 restraints weight = 191321.663| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.30 r_work: 0.2775 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 44376 Z= 0.138 Angle : 0.595 16.229 61299 Z= 0.309 Chirality : 0.042 0.270 7126 Planarity : 0.003 0.070 6810 Dihedral : 22.354 177.353 8407 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 24.53 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 4702 helix: 1.75 (0.11), residues: 2271 sheet: 0.40 (0.20), residues: 651 loop : -1.00 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 191 TYR 0.027 0.001 TYR H 86 PHE 0.023 0.001 PHE E 78 TRP 0.023 0.002 TRP Q1396 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (44375) covalent geometry : angle 0.59485 / 0.31 (61299) hydrogen bonds : bond 0.04015 / 2.60 ( 1963) hydrogen bonds : angle 3.51989 / 2.48 ( 5413) Misc. bond : bond 0.00408 / 0.27 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12526.49 seconds wall clock time: 214 minutes 31.00 seconds (12871.00 seconds total)