Starting phenix.real_space_refine on Fri Nov 21 04:06:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9t_45370/11_2025/9c9t_45370_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9t_45370/11_2025/9c9t_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_45370/11_2025/9c9t_45370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9t_45370/11_2025/9c9t_45370.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9t_45370/11_2025/9c9t_45370_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9t_45370/11_2025/9c9t_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 10.02, per 1000 atoms: 0.23 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: 3.55 Conformation dependent library (CDL) restraints added in 1.9 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: 5.85 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: 14.77 Time building geometry restraints manager: 4.87 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=" N VAL Y 96 " pdb=" CA VAL Y 96 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.70e-03 1.32e+04 1.79e+01 bond pdb=" CA GLN Q 874 " pdb=" C GLN Q 874 " ideal model delta sigma weight residual 1.522 1.589 -0.067 1.72e-02 3.38e+03 1.51e+01 bond pdb=" C1' DG I 32 " pdb=" N9 DG I 32 " ideal model delta sigma weight residual 1.460 1.393 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1' DA J -33 " pdb=" N9 DA J -33 " ideal model delta sigma weight residual 1.460 1.395 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C1' DG I -75 " pdb=" N9 DG I -75 " ideal model delta sigma weight residual 1.460 1.405 0.055 2.00e-02 2.50e+03 7.57e+00 ... (remaining 44370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 60878 4.22 - 8.44: 369 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=" 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 angle pdb=" C ASP W 218 " pdb=" CA ASP W 218 " pdb=" CB ASP W 218 " ideal model delta sigma weight residual 111.91 103.04 8.87 1.52e+00 4.33e-01 3.40e+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: 6884 0.117 - 0.233: 232 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: 8.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 49.110 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 : 0.004 0.067 44376 Z= 0.223 Angle : 0.901 21.098 61299 Z= 0.492 Chirality : 0.051 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 covalent geometry : bond 0.00448 (44375) covalent geometry : angle 0.90061 (61299) hydrogen bonds : bond 0.14682 ( 1963) hydrogen bonds : angle 5.94359 ( 5413) Misc. bond : bond 0.00170 ( 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 : 1.609 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: 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: 0.2905 time to fit residues: 124.9507 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 : 1.579 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 808 ASN Q 875 ASN Q1204 ASN Q1362 GLN Q1382 ASN R 144 GLN R 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.075653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047592 restraints weight = 191765.742| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.34 r_work: 0.2799 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 44376 Z= 0.208 Angle : 0.613 11.772 61299 Z= 0.327 Chirality : 0.041 0.185 7126 Planarity : 0.004 0.048 6810 Dihedral : 22.528 177.713 8407 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.04 % Allowed : 23.38 % 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: -0.41 (0.12), residues: 4702 helix: 0.40 (0.11), residues: 2286 sheet: 0.37 (0.20), residues: 670 loop : -1.35 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 102 TYR 0.033 0.001 TYR X 462 PHE 0.022 0.001 PHE R 691 TRP 0.016 0.002 TRP Q 755 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00474 (44375) covalent geometry : angle 0.61341 (61299) hydrogen bonds : bond 0.04879 ( 1963) hydrogen bonds : angle 3.95739 ( 5413) Misc. bond : bond 0.00307 ( 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 316 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 235 time to evaluate : 1.531 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: D 74 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8875 (pp20) REVERT: F 64 GLU cc_start: 0.9544 (tt0) cc_final: 0.9294 (mt-10) REVERT: G 65 GLU cc_start: 0.9234 (tp30) cc_final: 0.9008 (tp30) REVERT: H 59 GLN cc_start: 0.9241 (mp10) cc_final: 0.8980 (pm20) REVERT: Q 733 MET cc_start: 0.3532 (tpt) cc_final: 0.3103 (tpt) REVERT: R 149 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8445 (t0) REVERT: R 157 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8895 (p) REVERT: T 312 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: U 153 HIS cc_start: 0.8020 (t-90) cc_final: 0.7814 (p-80) REVERT: V 171 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9081 (ttpt) REVERT: X 312 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: X 444 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9193 (tt) REVERT: Y 279 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8965 (tp30) outliers start: 81 outliers final: 30 residues processed: 294 average time/residue: 0.2690 time to fit residues: 129.2774 Evaluate side-chains 252 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 25 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 826 ASP Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1324 MET 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 S residue 138 GLU Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 191 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 165 MET Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 202 LEU 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 200 THR Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 107 optimal weight: 3.9990 chunk 420 optimal weight: 0.4980 chunk 371 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 454 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** 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 = 0.3840 r_free = 0.3840 target = 0.075791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047840 restraints weight = 191429.085| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.38 r_work: 0.2803 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 44376 Z= 0.155 Angle : 0.570 11.943 61299 Z= 0.302 Chirality : 0.040 0.179 7126 Planarity : 0.004 0.074 6810 Dihedral : 22.389 179.124 8407 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.16 % Allowed : 23.58 % 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: 0.20 (0.12), residues: 4702 helix: 1.07 (0.11), residues: 2265 sheet: 0.42 (0.20), residues: 672 loop : -1.19 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 72 TYR 0.025 0.001 TYR X 462 PHE 0.020 0.001 PHE R 691 TRP 0.016 0.002 TRP Q 854 HIS 0.004 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00353 (44375) covalent geometry : angle 0.57017 (61299) hydrogen bonds : bond 0.04259 ( 1963) hydrogen bonds : angle 3.70970 ( 5413) Misc. bond : bond 0.00224 ( 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: 86 poor density : 231 time to evaluate : 1.440 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: 0.9159 (mm-30) cc_final: 0.8875 (pp20) REVERT: F 64 GLU cc_start: 0.9602 (tt0) cc_final: 0.9318 (tt0) REVERT: F 68 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8492 (mmp80) REVERT: G 105 GLN cc_start: 0.7496 (tm-30) cc_final: 0.7097 (tm-30) REVERT: H 59 GLN cc_start: 0.9265 (mp10) cc_final: 0.9023 (pm20) REVERT: H 96 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: Q 733 MET cc_start: 0.3410 (tpt) cc_final: 0.2850 (tpt) REVERT: Q 816 MET cc_start: 0.5667 (tpt) cc_final: 0.5465 (tpt) REVERT: Q 822 MET cc_start: 0.8021 (tpp) cc_final: 0.7708 (tpp) REVERT: R 157 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9014 (p) REVERT: R 749 ASN cc_start: 0.9493 (OUTLIER) cc_final: 0.8724 (m-40) REVERT: T 312 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: U 153 HIS cc_start: 0.8062 (t-90) cc_final: 0.7832 (p-80) REVERT: U 272 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: U 276 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9020 (ttmm) REVERT: V 171 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9066 (ttpt) REVERT: V 282 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8472 (tm-30) REVERT: V 355 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8618 (p) REVERT: W 182 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8439 (pp20) REVERT: X 312 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: X 444 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9222 (tt) REVERT: Y 86 MET cc_start: 0.9040 (tpp) cc_final: 0.8648 (tpp) REVERT: Y 279 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8964 (tp30) outliers start: 86 outliers final: 46 residues processed: 299 average time/residue: 0.2711 time to fit residues: 133.0504 Evaluate side-chains 277 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain Q residue 729 LEU 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 1089 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 Q residue 1324 MET Chi-restraints excluded: chain R residue 92 VAL 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 95 VAL 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 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 272 GLN Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 355 SER 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 125 PHE 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 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 279 GLU Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 168 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 365 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 464 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN F 76 HIS ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 132 ASN R 149 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.074863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047214 restraints weight = 191856.287| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.20 r_work: 0.2777 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 44376 Z= 0.204 Angle : 0.592 11.063 61299 Z= 0.312 Chirality : 0.041 0.206 7126 Planarity : 0.004 0.041 6810 Dihedral : 22.336 179.961 8407 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 3.17 % Allowed : 22.85 % Favored : 73.98 % 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: 0.48 (0.12), residues: 4702 helix: 1.39 (0.11), residues: 2269 sheet: 0.43 (0.20), residues: 662 loop : -1.13 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 36 TYR 0.030 0.001 TYR X 462 PHE 0.018 0.001 PHE R 691 TRP 0.025 0.002 TRP Q 854 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00468 (44375) covalent geometry : angle 0.59243 (61299) hydrogen bonds : bond 0.04598 ( 1963) hydrogen bonds : angle 3.69392 ( 5413) Misc. bond : bond 0.00210 ( 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 349 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 223 time to evaluate : 1.660 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: C 57 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: D 74 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8860 (pp20) REVERT: F 73 TYR cc_start: 0.8825 (m-80) cc_final: 0.8619 (m-10) REVERT: H 59 GLN cc_start: 0.9295 (mp10) cc_final: 0.9053 (pm20) REVERT: H 83 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9100 (tt) REVERT: H 123 LYS cc_start: 0.9414 (tttp) cc_final: 0.9212 (tttm) REVERT: Q 816 MET cc_start: 0.5792 (tpt) cc_final: 0.5516 (tpt) REVERT: Q 838 MET cc_start: 0.1314 (ptt) cc_final: -0.0080 (mtt) REVERT: R 157 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9074 (p) REVERT: R 749 ASN cc_start: 0.9511 (OUTLIER) cc_final: 0.8806 (m-40) REVERT: T 191 ARG cc_start: 0.9117 (tmm-80) cc_final: 0.8866 (tmm-80) REVERT: T 271 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7716 (tm-30) REVERT: T 312 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: U 23 HIS cc_start: 0.9180 (OUTLIER) cc_final: 0.8781 (p90) REVERT: U 243 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: U 363 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: V 171 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9085 (ttpt) REVERT: V 268 MET cc_start: 0.8890 (mtt) cc_final: 0.8677 (mtt) REVERT: V 282 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8537 (tm-30) REVERT: V 324 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9314 (tt) REVERT: V 355 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8676 (p) REVERT: W 182 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8446 (pp20) REVERT: X 294 LYS cc_start: 0.9511 (tppt) cc_final: 0.9270 (tppt) REVERT: X 312 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: X 444 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9223 (tt) REVERT: Y 86 MET cc_start: 0.9079 (tpp) cc_final: 0.8805 (tpp) REVERT: Y 104 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.9300 (t) REVERT: Y 279 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8897 (tp30) outliers start: 126 outliers final: 67 residues processed: 332 average time/residue: 0.2733 time to fit residues: 148.5235 Evaluate side-chains 295 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 212 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU 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 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 46 SER 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 729 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 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 R residue 92 VAL Chi-restraints excluded: chain R residue 137 THR 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 660 THR 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 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 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 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 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 195 SER 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 355 SER 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 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 388 THR 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 X residue 444 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 431 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 442 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 446 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN F 65 ASN ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.075437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.048243 restraints weight = 190629.544| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.17 r_work: 0.2811 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44376 Z= 0.136 Angle : 0.553 11.409 61299 Z= 0.292 Chirality : 0.040 0.174 7126 Planarity : 0.003 0.046 6810 Dihedral : 22.259 178.531 8407 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 2.51 % Allowed : 23.23 % 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: 0.68 (0.12), residues: 4702 helix: 1.58 (0.11), residues: 2264 sheet: 0.48 (0.20), residues: 662 loop : -1.05 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 191 TYR 0.022 0.001 TYR X 462 PHE 0.018 0.001 PHE R 691 TRP 0.018 0.001 TRP Q 854 HIS 0.007 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00306 (44375) covalent geometry : angle 0.55279 (61299) hydrogen bonds : bond 0.03911 ( 1963) hydrogen bonds : angle 3.52017 ( 5413) Misc. bond : bond 0.00430 ( 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 325 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 225 time to evaluate : 1.716 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: C 57 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: D 74 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8913 (pp20) REVERT: F 67 ILE cc_start: 0.8629 (tp) cc_final: 0.8115 (tt) REVERT: G 105 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7074 (tm-30) REVERT: H 59 GLN cc_start: 0.9295 (mp10) cc_final: 0.9048 (pm20) REVERT: H 112 HIS cc_start: 0.9190 (m90) cc_final: 0.8919 (m90) REVERT: H 123 LYS cc_start: 0.9419 (tttp) cc_final: 0.9182 (tttm) REVERT: Q 816 MET cc_start: 0.5770 (tpt) cc_final: 0.5468 (tpt) REVERT: Q 838 MET cc_start: 0.1186 (ptt) cc_final: -0.0048 (mtt) REVERT: R 687 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: R 749 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.8783 (m-40) REVERT: T 191 ARG cc_start: 0.9116 (tmm-80) cc_final: 0.8860 (tmm-80) REVERT: T 312 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: U 23 HIS cc_start: 0.9154 (OUTLIER) cc_final: 0.8725 (p90) REVERT: U 276 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8986 (ttmm) REVERT: V 171 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9052 (ttpt) REVERT: V 282 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8439 (tm-30) REVERT: V 324 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9311 (tt) REVERT: W 182 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8477 (pp20) REVERT: X 312 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: Y 86 MET cc_start: 0.9062 (tpp) cc_final: 0.8753 (tpp) REVERT: Y 104 SER cc_start: 0.9516 (OUTLIER) cc_final: 0.9275 (t) REVERT: Y 166 GLU cc_start: 0.8362 (tp30) cc_final: 0.8051 (tp30) REVERT: Y 279 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8864 (tp30) outliers start: 100 outliers final: 60 residues processed: 313 average time/residue: 0.2761 time to fit residues: 141.5910 Evaluate side-chains 281 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 209 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 729 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 1089 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 92 VAL Chi-restraints excluded: chain R residue 137 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 687 GLU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN 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 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 276 LYS Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 195 SER 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 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 230 VAL Chi-restraints excluded: chain X residue 312 GLU 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 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 117 optimal weight: 0.6980 chunk 227 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 302 optimal weight: 1.9990 chunk 301 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.074827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047739 restraints weight = 191895.791| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.40 r_work: 0.2773 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 44376 Z= 0.187 Angle : 0.584 11.086 61299 Z= 0.305 Chirality : 0.040 0.185 7126 Planarity : 0.003 0.042 6810 Dihedral : 22.208 177.877 8407 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 2.84 % Allowed : 23.25 % Favored : 73.91 % 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: 0.72 (0.13), residues: 4702 helix: 1.63 (0.11), residues: 2268 sheet: 0.46 (0.20), residues: 660 loop : -1.04 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 68 TYR 0.032 0.001 TYR H 86 PHE 0.017 0.001 PHE R 691 TRP 0.043 0.002 TRP Q1396 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd covalent geometry : bond 0.00432 (44375) covalent geometry : angle 0.58399 (61299) hydrogen bonds : bond 0.04284 ( 1963) hydrogen bonds : angle 3.58130 ( 5413) Misc. bond : bond 0.00475 ( 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 328 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 215 time to evaluate : 1.829 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: C 57 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: D 74 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8914 (pp20) REVERT: F 75 GLU cc_start: 0.9220 (pp20) cc_final: 0.8992 (pp20) REVERT: G 105 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7184 (tm-30) REVERT: H 59 GLN cc_start: 0.9306 (mp10) cc_final: 0.9088 (pm20) REVERT: Q 816 MET cc_start: 0.5830 (tpt) cc_final: 0.5525 (tpt) REVERT: Q 838 MET cc_start: 0.0973 (ptt) cc_final: -0.0185 (mtt) REVERT: R 687 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8713 (mt-10) REVERT: R 749 ASN cc_start: 0.9509 (OUTLIER) cc_final: 0.8801 (m-40) REVERT: T 191 ARG cc_start: 0.9164 (tmm-80) cc_final: 0.8904 (tmm-80) REVERT: T 312 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: U 23 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8732 (p90) REVERT: U 243 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: U 276 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9021 (ttmm) REVERT: V 171 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9087 (ttpt) REVERT: V 324 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9336 (tt) REVERT: W 182 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8836 (pp20) REVERT: X 312 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: X 373 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9150 (mm) REVERT: Y 86 MET cc_start: 0.9116 (tpp) cc_final: 0.8888 (tpp) REVERT: Y 104 SER cc_start: 0.9493 (OUTLIER) cc_final: 0.9263 (t) REVERT: Y 166 GLU cc_start: 0.8390 (tp30) cc_final: 0.8060 (tp30) REVERT: Y 279 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8883 (tp30) outliers start: 113 outliers final: 76 residues processed: 313 average time/residue: 0.2634 time to fit residues: 137.0181 Evaluate side-chains 298 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 208 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE 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 50 LEU Chi-restraints excluded: chain F residue 59 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 G residue 46 SER Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 729 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 752 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 1089 ILE Chi-restraints excluded: chain Q residue 1229 VAL 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 137 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 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 254 VAL 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 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 300 MET Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 195 SER 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 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 346 THR Chi-restraints excluded: chain X residue 373 LEU 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 200 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 152 optimal weight: 0.9980 chunk 446 optimal weight: 10.0000 chunk 262 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 425 optimal weight: 0.9990 chunk 299 optimal weight: 0.9990 chunk 391 optimal weight: 3.9990 chunk 453 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** Q 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1180 ASN R 213 ASN R 635 GLN S 162 ASN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.076011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048304 restraints weight = 190158.019| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.20 r_work: 0.2824 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 44376 Z= 0.111 Angle : 0.554 18.601 61299 Z= 0.288 Chirality : 0.039 0.164 7126 Planarity : 0.003 0.041 6810 Dihedral : 22.070 177.068 8407 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.16 % Allowed : 23.96 % 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: 0.84 (0.13), residues: 4702 helix: 1.73 (0.11), residues: 2264 sheet: 0.56 (0.20), residues: 666 loop : -0.99 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 191 TYR 0.033 0.001 TYR H 86 PHE 0.017 0.001 PHE R 691 TRP 0.033 0.002 TRP Q1396 HIS 0.006 0.001 HIS U 153 Details of bonding type rmsd covalent geometry : bond 0.00246 (44375) covalent geometry : angle 0.55388 (61299) hydrogen bonds : bond 0.03530 ( 1963) hydrogen bonds : angle 3.35984 ( 5413) Misc. bond : bond 0.00359 ( 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 314 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 228 time to evaluate : 1.367 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: A 64 LYS cc_start: 0.9196 (tptt) cc_final: 0.8899 (mmmt) REVERT: C 57 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: D 74 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8906 (pp20) REVERT: F 67 ILE cc_start: 0.8699 (tp) cc_final: 0.7872 (tt) REVERT: F 68 ARG cc_start: 0.9140 (mmm160) cc_final: 0.8710 (mmp80) REVERT: F 75 GLU cc_start: 0.9257 (pp20) cc_final: 0.9032 (pp20) REVERT: G 105 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7370 (tm-30) REVERT: H 59 GLN cc_start: 0.9296 (mp10) cc_final: 0.9063 (pm20) REVERT: H 96 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: Q 816 MET cc_start: 0.5844 (tpt) cc_final: 0.5565 (tpt) REVERT: R 157 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9075 (p) REVERT: R 749 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.8827 (m-40) REVERT: S 78 LEU cc_start: 0.9591 (tp) cc_final: 0.9271 (pp) REVERT: T 191 ARG cc_start: 0.9128 (tmm-80) cc_final: 0.8872 (tmm-80) REVERT: T 312 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: U 23 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8678 (p90) REVERT: U 243 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: U 276 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8953 (ttmm) REVERT: V 282 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8428 (tm-30) REVERT: W 182 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8474 (pp20) REVERT: X 373 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9111 (mm) REVERT: Y 86 MET cc_start: 0.9083 (tpp) cc_final: 0.8786 (tpp) REVERT: Y 279 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.8866 (tp30) outliers start: 86 outliers final: 52 residues processed: 297 average time/residue: 0.2693 time to fit residues: 129.4388 Evaluate side-chains 274 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 80 LYS Chi-restraints excluded: chain C residue 57 GLU 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 59 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 729 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 752 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 R residue 67 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 ASN 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 95 VAL Chi-restraints excluded: chain T residue 71 SER 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 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 175 MET Chi-restraints excluded: chain U residue 215 MET 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 195 SER Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain W residue 65 THR 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 373 LEU Chi-restraints excluded: chain Y residue 89 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 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 195 optimal weight: 8.9990 chunk 273 optimal weight: 3.9990 chunk 385 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 451 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 421 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 479 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.075130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047611 restraints weight = 191560.717| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.25 r_work: 0.2793 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2211 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= 0.159 Angle : 0.575 14.536 61299 Z= 0.299 Chirality : 0.040 0.157 7126 Planarity : 0.003 0.040 6810 Dihedral : 22.033 177.492 8407 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.44 % Allowed : 23.78 % Favored : 73.78 % 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: 0.90 (0.13), residues: 4702 helix: 1.80 (0.11), residues: 2265 sheet: 0.51 (0.20), residues: 664 loop : -0.95 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 102 TYR 0.037 0.001 TYR H 86 PHE 0.018 0.001 PHE R 234 TRP 0.025 0.002 TRP Q1396 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00365 (44375) covalent geometry : angle 0.57532 (61299) hydrogen bonds : bond 0.04026 ( 1963) hydrogen bonds : angle 3.44051 ( 5413) Misc. bond : bond 0.00404 ( 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 314 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 217 time to evaluate : 1.507 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 36 ARG cc_start: 0.3558 (OUTLIER) cc_final: 0.2032 (tpt-90) REVERT: D 74 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8906 (pp20) REVERT: F 67 ILE cc_start: 0.8711 (tp) cc_final: 0.7920 (tt) REVERT: F 68 ARG cc_start: 0.9168 (mmm160) cc_final: 0.8790 (mmp80) REVERT: F 75 GLU cc_start: 0.9267 (pp20) cc_final: 0.9064 (pp20) REVERT: H 82 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8832 (ttpp) REVERT: H 86 TYR cc_start: 0.8311 (m-10) cc_final: 0.7987 (m-10) REVERT: H 96 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: Q 816 MET cc_start: 0.5880 (tpt) cc_final: 0.5576 (tpt) REVERT: R 157 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9107 (p) REVERT: S 78 LEU cc_start: 0.9606 (tp) cc_final: 0.9324 (pp) REVERT: T 191 ARG cc_start: 0.9146 (tmm-80) cc_final: 0.8890 (tmm-80) REVERT: T 312 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: U 23 HIS cc_start: 0.9172 (OUTLIER) cc_final: 0.8695 (p90) REVERT: U 243 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: U 276 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9003 (ttmm) REVERT: U 421 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8845 (pt0) REVERT: V 141 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9041 (pm20) REVERT: V 282 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8466 (tm-30) REVERT: V 324 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9330 (tt) REVERT: W 182 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8868 (pp20) REVERT: X 373 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9139 (mm) REVERT: Y 86 MET cc_start: 0.9144 (tpp) cc_final: 0.8906 (tpp) REVERT: Y 279 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.8864 (tp30) outliers start: 97 outliers final: 69 residues processed: 300 average time/residue: 0.2443 time to fit residues: 120.3080 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 : 1.224 ------------------------------------------------------------------------------- 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 80 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 36 ARG 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 18 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 752 HIS Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 1007 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 R residue 67 LEU Chi-restraints excluded: chain R residue 80 THR 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 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 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 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 175 MET 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 421 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 141 GLU Chi-restraints excluded: chain V residue 195 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 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 181 LEU Chi-restraints excluded: chain X residue 230 VAL 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 249 SER Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 233 optimal weight: 6.9990 chunk 393 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 312 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 355 optimal weight: 0.9980 chunk 196 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** Q 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1180 ASN ** V 165 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.075437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.047550 restraints weight = 190253.906| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.29 r_work: 0.2787 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44376 Z= 0.132 Angle : 0.573 15.880 61299 Z= 0.296 Chirality : 0.039 0.214 7126 Planarity : 0.003 0.045 6810 Dihedral : 21.997 177.446 8407 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 2.19 % Allowed : 24.28 % Favored : 73.53 % 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: 0.93 (0.13), residues: 4702 helix: 1.81 (0.11), residues: 2266 sheet: 0.57 (0.20), residues: 662 loop : -0.95 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 191 TYR 0.026 0.001 TYR H 86 PHE 0.016 0.001 PHE R 691 TRP 0.026 0.002 TRP Q1396 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00302 (44375) covalent geometry : angle 0.57343 (61299) hydrogen bonds : bond 0.03699 ( 1963) hydrogen bonds : angle 3.38504 ( 5413) Misc. bond : bond 0.00358 ( 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 305 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 218 time to evaluate : 1.238 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: B 91 LEU cc_start: 0.9692 (mm) cc_final: 0.9274 (tp) REVERT: B 96 ARG cc_start: 0.9351 (mtp180) cc_final: 0.8912 (mtp180) REVERT: D 36 ARG cc_start: 0.3469 (OUTLIER) cc_final: 0.2082 (tpt-90) REVERT: D 74 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8887 (pp20) REVERT: F 67 ILE cc_start: 0.8689 (tp) cc_final: 0.7924 (tt) REVERT: F 68 ARG cc_start: 0.9171 (mmm160) cc_final: 0.8850 (mmp80) REVERT: F 75 GLU cc_start: 0.9305 (pp20) cc_final: 0.9097 (pp20) REVERT: F 89 TYR cc_start: 0.8379 (m-10) cc_final: 0.7961 (m-80) REVERT: G 105 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7238 (pp30) REVERT: H 96 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: Q 816 MET cc_start: 0.5920 (tpt) cc_final: 0.5614 (tpt) REVERT: R 157 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9114 (p) REVERT: R 749 ASN cc_start: 0.9519 (OUTLIER) cc_final: 0.8815 (m-40) REVERT: S 78 LEU cc_start: 0.9617 (tp) cc_final: 0.9346 (pp) REVERT: S 131 ASN cc_start: 0.9329 (m-40) cc_final: 0.9019 (t0) REVERT: T 191 ARG cc_start: 0.9148 (tmm-80) cc_final: 0.8891 (tmm-80) REVERT: T 312 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: U 23 HIS cc_start: 0.9180 (OUTLIER) cc_final: 0.8697 (p90) REVERT: U 243 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: U 276 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8962 (ttmm) REVERT: U 421 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8855 (pt0) REVERT: V 141 GLU cc_start: 0.9463 (OUTLIER) cc_final: 0.9049 (pm20) REVERT: V 282 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8466 (tm-30) REVERT: W 182 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8877 (pp20) REVERT: X 373 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9100 (mm) REVERT: Y 86 MET cc_start: 0.9109 (tpp) cc_final: 0.8825 (tpp) REVERT: Y 279 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.8873 (tp30) outliers start: 87 outliers final: 68 residues processed: 294 average time/residue: 0.2505 time to fit residues: 119.1129 Evaluate side-chains 290 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 80 LYS Chi-restraints excluded: chain D residue 36 ARG 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 66 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 729 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 752 HIS Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1007 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 1229 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 80 THR 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 T residue 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 108 SER 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 175 MET 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 421 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 141 GLU Chi-restraints excluded: chain V residue 195 SER Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL 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 181 LEU Chi-restraints excluded: chain X residue 230 VAL 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 249 SER Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 89 optimal weight: 10.0000 chunk 365 optimal weight: 0.0170 chunk 341 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 434 optimal weight: 0.1980 chunk 435 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 chunk 466 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 414 optimal weight: 9.9990 overall best weight: 1.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.075589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.046838 restraints weight = 188281.965| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.12 r_work: 0.2805 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44376 Z= 0.131 Angle : 0.572 16.312 61299 Z= 0.295 Chirality : 0.039 0.179 7126 Planarity : 0.003 0.044 6810 Dihedral : 21.935 177.761 8407 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.24 % Allowed : 24.28 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.13), residues: 4702 helix: 1.83 (0.11), residues: 2269 sheet: 0.59 (0.20), residues: 662 loop : -0.93 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 102 TYR 0.018 0.001 TYR X 462 PHE 0.016 0.001 PHE R 691 TRP 0.034 0.002 TRP Q1396 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00299 (44375) covalent geometry : angle 0.57247 (61299) hydrogen bonds : bond 0.03707 ( 1963) hydrogen bonds : angle 3.35615 ( 5413) Misc. bond : bond 0.00356 ( 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 309 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 1.587 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: A 42 LYS cc_start: 0.5129 (tppt) cc_final: 0.4666 (tptt) REVERT: B 91 LEU cc_start: 0.9705 (mm) cc_final: 0.9311 (tp) REVERT: B 96 ARG cc_start: 0.9323 (mtp180) cc_final: 0.8929 (mtp85) REVERT: D 36 ARG cc_start: 0.3528 (OUTLIER) cc_final: 0.2096 (tpt-90) REVERT: D 74 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8884 (pp20) REVERT: F 67 ILE cc_start: 0.8725 (tp) cc_final: 0.7995 (tt) REVERT: F 68 ARG cc_start: 0.9182 (mmm160) cc_final: 0.8899 (mmp80) REVERT: F 75 GLU cc_start: 0.9296 (pp20) cc_final: 0.9089 (pp20) REVERT: G 105 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7263 (pp30) REVERT: H 96 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: Q 816 MET cc_start: 0.5901 (tpt) cc_final: 0.5604 (tpt) REVERT: Q 822 MET cc_start: 0.7754 (tpp) cc_final: 0.7518 (tpp) REVERT: R 157 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.9109 (p) REVERT: R 749 ASN cc_start: 0.9515 (OUTLIER) cc_final: 0.8809 (m-40) REVERT: S 78 LEU cc_start: 0.9604 (tp) cc_final: 0.9335 (pp) REVERT: S 131 ASN cc_start: 0.9320 (m-40) cc_final: 0.9006 (t0) REVERT: T 191 ARG cc_start: 0.9143 (tmm-80) cc_final: 0.8896 (tmm-80) REVERT: T 312 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: U 23 HIS cc_start: 0.9174 (OUTLIER) cc_final: 0.8707 (p90) REVERT: U 243 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: U 276 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8968 (ttmm) REVERT: U 421 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8841 (pt0) REVERT: V 141 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9040 (pm20) REVERT: V 282 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8432 (tm-30) REVERT: W 182 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8875 (pp20) REVERT: X 373 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9102 (mm) REVERT: Y 86 MET cc_start: 0.9108 (tpp) cc_final: 0.8822 (tpp) REVERT: Y 279 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.8838 (tp30) outliers start: 89 outliers final: 69 residues processed: 298 average time/residue: 0.2275 time to fit residues: 112.1643 Evaluate side-chains 292 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 80 LYS Chi-restraints excluded: chain D residue 36 ARG 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 81 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 747 HIS Chi-restraints excluded: chain Q residue 752 HIS Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1007 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 1229 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1324 MET Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 80 THR 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 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 108 SER 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 175 MET 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 421 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 141 GLU Chi-restraints excluded: chain V residue 195 SER Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL 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 181 LEU Chi-restraints excluded: chain X residue 230 VAL 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 249 SER Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 441 optimal weight: 0.0060 chunk 400 optimal weight: 0.5980 chunk 397 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 343 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN Q1180 ASN Q1443 GLN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.075878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.048066 restraints weight = 190056.014| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.32 r_work: 0.2806 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44376 Z= 0.120 Angle : 0.569 16.412 61299 Z= 0.293 Chirality : 0.039 0.170 7126 Planarity : 0.003 0.041 6810 Dihedral : 21.874 177.723 8407 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.14 % Allowed : 24.33 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4702 helix: 1.85 (0.11), residues: 2270 sheet: 0.62 (0.20), residues: 661 loop : -0.90 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 191 TYR 0.017 0.001 TYR X 462 PHE 0.016 0.001 PHE R 691 TRP 0.029 0.002 TRP Q1396 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00271 (44375) covalent geometry : angle 0.56897 (61299) hydrogen bonds : bond 0.03549 ( 1963) hydrogen bonds : angle 3.29930 ( 5413) Misc. bond : bond 0.00333 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12435.54 seconds wall clock time: 212 minutes 21.52 seconds (12741.52 seconds total)