Starting phenix.real_space_refine on Tue Jul 7 05:21:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9t_45370/07_2026/9c9t_45370_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9t_45370/07_2026/9c9t_45370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9t_45370/07_2026/9c9t_45370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9t_45370/07_2026/9c9t_45370.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9t_45370/07_2026/9c9t_45370_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9t_45370/07_2026/9c9t_45370_neut.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 306 5.49 5 S 108 5.16 5 C 26188 2.51 5 N 7628 2.21 5 O 8854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43084 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3030 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2997 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "Q" Number of atoms: 5278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5278 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 30, 'TRANS': 628} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3963 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 28, 'TRANS': 496} Chain breaks: 4 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 176 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "Y" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 387 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.44, per 1000 atoms: 0.22 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: 3.09 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: 6.08 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: 17.61 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9412 1.33 - 1.46: 10976 1.46 - 1.58: 23191 1.58 - 1.70: 605 1.70 - 1.83: 191 Bond restraints: 44375 Sorted by residual: bond pdb=" C1' DC J 75 " pdb=" N1 DC J 75 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.45e+01 bond pdb=" C1' DT J 73 " pdb=" N1 DT J 73 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.30e+01 bond pdb=" C1' DT J 68 " pdb=" N1 DT J 68 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" C1' DT J 71 " pdb=" N1 DT J 71 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" C1' DC J 66 " pdb=" N1 DC J 66 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.19e+01 ... (remaining 44370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 60876 4.22 - 8.44: 371 8.44 - 12.66: 45 12.66 - 16.88: 6 16.88 - 21.10: 1 Bond angle restraints: 61299 Sorted by residual: angle pdb=" N ASP W 218 " pdb=" CA ASP W 218 " pdb=" C ASP W 218 " ideal model delta sigma weight residual 110.70 95.86 14.84 1.55e+00 4.16e-01 9.17e+01 angle pdb=" C MET W 215 " pdb=" CA MET W 215 " pdb=" CB MET W 215 " ideal model delta sigma weight residual 116.54 108.88 7.66 1.15e+00 7.56e-01 4.44e+01 angle pdb=" O4' DC I -26 " pdb=" C4' DC I -26 " pdb=" C3' DC I -26 " ideal model delta sigma weight residual 106.00 102.38 3.62 6.00e-01 2.78e+00 3.65e+01 angle pdb=" CA LEU H 48 " pdb=" CB LEU H 48 " pdb=" CG LEU H 48 " ideal model delta sigma weight residual 116.30 137.40 -21.10 3.50e+00 8.16e-02 3.63e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.43 107.03 6.40 1.09e+00 8.42e-01 3.45e+01 ... (remaining 61294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 24073 35.81 - 71.61: 2118 71.61 - 107.42: 77 107.42 - 143.23: 2 143.23 - 179.03: 2 Dihedral angle restraints: 26272 sinusoidal: 12500 harmonic: 13772 Sorted by residual: dihedral pdb=" C ASP W 218 " pdb=" N ASP W 218 " pdb=" CA ASP W 218 " pdb=" CB ASP W 218 " ideal model delta harmonic sigma weight residual -122.60 -106.39 -16.21 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" O2A ADP T1001 " pdb=" O3A ADP T1001 " pdb=" PA ADP T1001 " pdb=" PB ADP T1001 " ideal model delta sinusoidal sigma weight residual -60.00 50.96 -110.96 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" CA LEU X 181 " pdb=" C LEU X 181 " pdb=" N ASP X 182 " pdb=" CA ASP X 182 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 26269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 6873 0.117 - 0.233: 243 0.233 - 0.350: 7 0.350 - 0.466: 2 0.466 - 0.583: 1 Chirality restraints: 7126 Sorted by residual: chirality pdb=" CA ASP W 218 " pdb=" N ASP W 218 " pdb=" C ASP W 218 " pdb=" CB ASP W 218 " both_signs ideal model delta sigma weight residual False 2.51 3.09 -0.58 2.00e-01 2.50e+01 8.49e+00 chirality pdb=" CG LEU S 78 " pdb=" CB LEU S 78 " pdb=" CD1 LEU S 78 " pdb=" CD2 LEU S 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE Q 873 " pdb=" CA ILE Q 873 " pdb=" CG1 ILE Q 873 " pdb=" CG2 ILE Q 873 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 7123 not shown) Planarity restraints: 6810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG W 220 " -0.448 9.50e-02 1.11e+02 2.01e-01 2.47e+01 pdb=" NE ARG W 220 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG W 220 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG W 220 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG W 220 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 105 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C GLN G 105 " -0.063 2.00e-02 2.50e+03 pdb=" O GLN G 105 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY G 106 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG W 208 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ARG W 208 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG W 208 " 0.022 2.00e-02 2.50e+03 pdb=" N SER W 209 " 0.019 2.00e-02 2.50e+03 ... (remaining 6807 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 109 2.43 - 3.05: 22860 3.05 - 3.66: 67741 3.66 - 4.28: 98149 4.28 - 4.90: 157306 Nonbonded interactions: 346165 Sorted by model distance: nonbonded pdb=" CD1 LEU W 185 " pdb=" CE MET W 215 " model vdw 1.811 3.880 nonbonded pdb=" OG SER X 355 " pdb=" O VAL X 359 " model vdw 2.251 3.040 nonbonded pdb=" O GLY B 100 " pdb=" OG SER H 63 " model vdw 2.269 3.040 nonbonded pdb=" N2 DG I 29 " pdb=" O2 DC J -29 " model vdw 2.283 2.496 nonbonded pdb=" O THR W 262 " pdb=" OG1 THR W 262 " model vdw 2.286 3.040 ... (remaining 346160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'T' and resid 22 through 1001) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 1001)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 1001)) } ncs_group { reference = (chain 'U' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 459 or \ resid 1001)) selection = (chain 'W' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 1001)) \ selection = (chain 'Y' and (resid 18 through 459 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.890 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: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 52.180 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 44376 Z= 0.370 Angle : 0.937 21.098 61299 Z= 0.594 Chirality : 0.052 0.583 7126 Planarity : 0.007 0.201 6810 Dihedral : 22.103 179.032 17370 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 25.79 % Favored : 74.21 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.11), residues: 4702 helix: -1.32 (0.09), residues: 2234 sheet: 0.20 (0.20), residues: 677 loop : -1.55 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG V 191 TYR 0.041 0.002 TYR C 40 PHE 0.047 0.002 PHE D 68 TRP 0.035 0.003 TRP Q 854 HIS 0.007 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.37 (44375) covalent geometry : angle 0.93671 / 0.59 (61299) hydrogen bonds : bond 0.14682 / 10.00 ( 1963) hydrogen bonds : angle 5.94359 / 4.17 ( 5413) Misc. bond : bond 0.00170 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9404 Ramachandran restraints generated. 4702 Oldfield, 0 Emsley, 4702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.585 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: 0.2790 time to fit residues: 119.9654 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 : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 50 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 R 745 HIS V 427 GLN W 36 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.075886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.048112 restraints weight = 191622.305| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.32 r_work: 0.2807 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 44376 Z= 0.203 Angle : 0.642 12.263 61299 Z= 0.344 Chirality : 0.044 0.261 7126 Planarity : 0.004 0.047 6810 Dihedral : 22.774 178.364 8407 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.73 % Allowed : 23.58 % Favored : 74.69 % 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: -0.47 (0.12), residues: 4702 helix: 0.34 (0.11), residues: 2284 sheet: 0.33 (0.20), residues: 670 loop : -1.35 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 102 TYR 0.030 0.001 TYR X 462 PHE 0.020 0.001 PHE R 691 TRP 0.017 0.001 TRP Q 854 HIS 0.005 0.001 HIS R 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (44375) covalent geometry : angle 0.64247 / 0.34 (61299) hydrogen bonds : bond 0.05268 / 3.40 ( 1963) hydrogen bonds : angle 4.06744 / 2.86 ( 5413) Misc. bond : bond 0.00357 / 0.24 ( 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 306 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 237 time to evaluate : 1.361 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: 0.9145 (mm-30) cc_final: 0.8876 (pp20) REVERT: H 59 GLN cc_start: 0.9236 (mp10) cc_final: 0.8963 (pm20) REVERT: Q 733 MET cc_start: 0.3303 (tpt) cc_final: 0.2905 (tpt) REVERT: S 131 ASN cc_start: 0.9333 (m-40) cc_final: 0.9128 (m110) REVERT: U 276 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9074 (ttmm) REVERT: V 171 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9094 (ttpt) REVERT: Y 279 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.8859 (tp30) outliers start: 69 outliers final: 31 residues processed: 284 average time/residue: 0.2497 time to fit residues: 116.5082 Evaluate side-chains 250 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain Q residue 729 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 125 VAL Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 107 optimal weight: 9.9990 chunk 420 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 454 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 393 optimal weight: 0.0670 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN G 42 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.076173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048800 restraints weight = 190068.331| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.46 r_work: 0.2814 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44376 Z= 0.133 Angle : 0.578 12.888 61299 Z= 0.310 Chirality : 0.042 0.250 7126 Planarity : 0.003 0.044 6810 Dihedral : 22.661 178.340 8407 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.19 % Allowed : 23.66 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.11 (0.12), residues: 4702 helix: 0.96 (0.11), residues: 2285 sheet: 0.45 (0.20), residues: 670 loop : -1.23 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 72 TYR 0.023 0.001 TYR X 462 PHE 0.020 0.001 PHE R 691 TRP 0.016 0.001 TRP Q 854 HIS 0.005 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (44375) covalent geometry : angle 0.57761 / 0.31 (61299) hydrogen bonds : bond 0.04471 / 2.88 ( 1963) hydrogen bonds : angle 3.76635 / 2.65 ( 5413) Misc. bond : bond 0.00285 / 0.19 ( 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 319 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 232 time to evaluate : 1.160 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: 0.9139 (mm-30) cc_final: 0.8868 (pp20) REVERT: H 59 GLN cc_start: 0.9244 (mp10) cc_final: 0.8998 (pm20) REVERT: H 112 HIS cc_start: 0.9273 (m90) cc_final: 0.8979 (m90) REVERT: H 123 LYS cc_start: 0.9487 (tttp) cc_final: 0.9185 (tmtt) REVERT: Q 733 MET cc_start: 0.3429 (tpt) cc_final: 0.2952 (tpt) REVERT: Q 822 MET cc_start: 0.7989 (tpp) cc_final: 0.7681 (tpp) REVERT: Q 838 MET cc_start: 0.0774 (ptt) cc_final: -0.0410 (mtt) REVERT: R 149 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8502 (t0) REVERT: R 157 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8937 (p) REVERT: S 78 LEU cc_start: 0.9619 (tp) cc_final: 0.9341 (pp) REVERT: U 272 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8707 (mt0) REVERT: V 171 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9047 (ttpt) REVERT: V 282 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8422 (tm-30) REVERT: W 182 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8918 (pp20) REVERT: X 312 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: Y 86 MET cc_start: 0.9006 (tpp) cc_final: 0.8641 (tpp) REVERT: Y 279 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8952 (tp30) outliers start: 87 outliers final: 42 residues processed: 297 average time/residue: 0.2484 time to fit residues: 121.6208 Evaluate side-chains 267 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 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 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 272 GLN Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 202 LEU Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 279 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 168 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 365 optimal weight: 1.9990 chunk 88 optimal weight: 50.0000 chunk 118 optimal weight: 30.0000 chunk 464 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 392 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 79 optimal weight: 50.0000 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q1359 HIS T 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.076069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048449 restraints weight = 191650.055| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.26 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44376 Z= 0.142 Angle : 0.573 12.735 61299 Z= 0.306 Chirality : 0.042 0.252 7126 Planarity : 0.003 0.040 6810 Dihedral : 22.598 178.328 8407 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.34 % Allowed : 23.88 % 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: 0.43 (0.12), residues: 4702 helix: 1.32 (0.11), residues: 2263 sheet: 0.48 (0.20), residues: 670 loop : -1.14 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 36 TYR 0.024 0.001 TYR X 462 PHE 0.019 0.001 PHE R 691 TRP 0.021 0.002 TRP Q 854 HIS 0.013 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (44375) covalent geometry : angle 0.57309 / 0.31 (61299) hydrogen bonds : bond 0.04287 / 2.77 ( 1963) hydrogen bonds : angle 3.63416 / 2.55 ( 5413) Misc. bond : bond 0.00507 / 0.34 ( 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 322 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 229 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.9514 (mmm-85) cc_final: 0.9138 (mtp85) REVERT: D 74 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8885 (pp20) REVERT: F 85 MET cc_start: 0.8703 (ppp) cc_final: 0.8502 (ppp) REVERT: H 59 GLN cc_start: 0.9275 (mp10) cc_final: 0.9007 (pm20) REVERT: H 123 LYS cc_start: 0.9439 (tttp) cc_final: 0.9130 (tmtt) REVERT: Q 822 MET cc_start: 0.8109 (tpp) cc_final: 0.7906 (tpp) REVERT: Q 838 MET cc_start: 0.0864 (ptt) cc_final: -0.0241 (mtt) REVERT: R 149 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8492 (t0) REVERT: R 157 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8985 (p) REVERT: R 749 ASN cc_start: 0.9479 (OUTLIER) cc_final: 0.8712 (m-40) REVERT: S 78 LEU cc_start: 0.9601 (tp) cc_final: 0.9324 (pp) REVERT: T 191 ARG cc_start: 0.9084 (tmm-80) cc_final: 0.8350 (tmm-80) REVERT: T 271 GLN cc_start: 0.8032 (tm130) cc_final: 0.7726 (tm-30) REVERT: T 312 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: U 276 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9025 (ttmm) REVERT: V 171 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9062 (ttpt) REVERT: V 268 MET cc_start: 0.8833 (mtt) cc_final: 0.8598 (mtt) REVERT: W 182 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8909 (pp20) REVERT: X 312 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: Y 86 MET cc_start: 0.9001 (tpp) cc_final: 0.8662 (tpp) REVERT: Y 104 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.9261 (t) REVERT: Y 279 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.8860 (tp30) outliers start: 93 outliers final: 54 residues processed: 308 average time/residue: 0.2650 time to fit residues: 135.1272 Evaluate side-chains 273 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain 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 74 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 729 LEU Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 869 THR Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1007 PHE Chi-restraints excluded: chain Q residue 1017 PHE Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1308 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 714 MET Chi-restraints excluded: chain R residue 749 ASN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 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 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 200 THR Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 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 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: 6.9990 chunk 203 optimal weight: 0.0070 chunk 148 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 442 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 446 optimal weight: 9.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN F 65 ASN F 76 HIS G 42 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 653 GLN ** S 162 ASN ** 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 = 0.3853 r_free = 0.3853 target = 0.076364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048581 restraints weight = 191326.459| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.29 r_work: 0.2826 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 44376 Z= 0.117 Angle : 0.558 12.823 61299 Z= 0.298 Chirality : 0.041 0.253 7126 Planarity : 0.003 0.041 6810 Dihedral : 22.489 177.902 8407 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 23.78 % Favored : 73.71 % 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: 0.60 (0.12), residues: 4702 helix: 1.50 (0.11), residues: 2262 sheet: 0.50 (0.20), residues: 660 loop : -1.09 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 36 TYR 0.020 0.001 TYR X 462 PHE 0.018 0.001 PHE R 691 TRP 0.033 0.002 TRP Q1396 HIS 0.010 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (44375) covalent geometry : angle 0.55797 / 0.30 (61299) hydrogen bonds : bond 0.04003 / 2.58 ( 1963) hydrogen bonds : angle 3.52793 / 2.48 ( 5413) Misc. bond : bond 0.00102 / 0.07 ( 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 329 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 229 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.9510 (mmm-85) cc_final: 0.9136 (mtp85) REVERT: C 57 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: D 74 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8880 (pp20) REVERT: F 64 GLU cc_start: 0.9596 (tt0) cc_final: 0.9389 (mt-10) REVERT: F 85 MET cc_start: 0.8669 (ppp) cc_final: 0.8455 (ppp) REVERT: G 105 GLN cc_start: 0.7553 (tm-30) cc_final: 0.6995 (tm-30) REVERT: H 59 GLN cc_start: 0.9269 (mp10) cc_final: 0.9010 (pm20) REVERT: H 112 HIS cc_start: 0.9210 (m90) cc_final: 0.8916 (m90) REVERT: H 123 LYS cc_start: 0.9415 (tttp) cc_final: 0.9096 (tmtt) REVERT: Q 822 MET cc_start: 0.8092 (tpp) cc_final: 0.7836 (tpp) REVERT: Q 838 MET cc_start: 0.0868 (ptt) cc_final: -0.0232 (mtt) REVERT: R 149 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8522 (t0) REVERT: R 157 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9027 (p) REVERT: R 749 ASN cc_start: 0.9482 (OUTLIER) cc_final: 0.8747 (m-40) REVERT: S 78 LEU cc_start: 0.9601 (tp) cc_final: 0.9325 (pp) REVERT: T 191 ARG cc_start: 0.9089 (tmm-80) cc_final: 0.8746 (tmm-80) REVERT: T 271 GLN cc_start: 0.8018 (tm130) cc_final: 0.7810 (tm-30) REVERT: T 312 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: U 276 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9023 (ttmm) REVERT: V 171 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9047 (ttpt) REVERT: V 282 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8389 (tm-30) REVERT: V 324 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9313 (tt) REVERT: W 182 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8451 (pp20) REVERT: X 312 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: Y 86 MET cc_start: 0.9069 (tpp) cc_final: 0.8755 (tpp) REVERT: Y 104 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9247 (t) REVERT: Y 279 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8853 (tp30) outliers start: 100 outliers final: 51 residues processed: 311 average time/residue: 0.2730 time to fit residues: 140.1544 Evaluate side-chains 278 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain 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 102 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 789 ASN Chi-restraints excluded: chain Q residue 948 ILE 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 92 VAL Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 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 108 SER Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain Y residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 117 optimal weight: 40.0000 chunk 227 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 90 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 301 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 326 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 132 ASN ** S 162 ASN ** 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 = 0.3817 r_free = 0.3817 target = 0.074697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.046787 restraints weight = 192499.098| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.34 r_work: 0.2768 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 44376 Z= 0.228 Angle : 0.629 12.058 61299 Z= 0.330 Chirality : 0.043 0.250 7126 Planarity : 0.004 0.041 6810 Dihedral : 22.553 178.843 8407 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 2.79 % Allowed : 23.33 % 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: 0.61 (0.12), residues: 4702 helix: 1.55 (0.11), residues: 2271 sheet: 0.46 (0.20), residues: 656 loop : -1.11 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 350 TYR 0.033 0.002 TYR X 462 PHE 0.016 0.001 PHE R 691 TRP 0.024 0.002 TRP Q1396 HIS 0.012 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (44375) covalent geometry : angle 0.62946 / 0.33 (61299) hydrogen bonds : bond 0.04978 / 3.29 ( 1963) hydrogen bonds : angle 3.72064 / 2.62 ( 5413) Misc. bond : bond 0.00505 / 0.34 ( 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 331 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 220 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.9694 (mm) cc_final: 0.9302 (tp) REVERT: D 74 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8929 (pp20) REVERT: E 82 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9174 (tp) REVERT: F 67 ILE cc_start: 0.8657 (tp) cc_final: 0.8101 (tt) REVERT: F 68 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8820 (mmm160) REVERT: F 85 MET cc_start: 0.8653 (ppp) cc_final: 0.8410 (ppp) REVERT: H 59 GLN cc_start: 0.9304 (mp10) cc_final: 0.9082 (pm20) REVERT: H 83 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9064 (tt) REVERT: Q 833 MET cc_start: 0.5468 (mmp) cc_final: 0.5209 (mmp) REVERT: Q 838 MET cc_start: 0.0896 (ptt) cc_final: -0.0149 (mtt) REVERT: R 149 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8524 (t0) REVERT: R 157 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9057 (p) REVERT: R 749 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.8747 (m-40) REVERT: T 191 ARG cc_start: 0.9138 (tmm-80) cc_final: 0.8492 (tmm-80) REVERT: T 312 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: U 175 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8154 (mmp) REVERT: U 243 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: U 276 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9038 (ttmm) REVERT: V 324 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9300 (tt) REVERT: W 182 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8871 (pp20) REVERT: X 312 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: Y 86 MET cc_start: 0.9125 (tpp) cc_final: 0.8890 (tpp) REVERT: Y 104 SER cc_start: 0.9541 (OUTLIER) cc_final: 0.9287 (t) REVERT: Y 279 GLU cc_start: 0.9404 (OUTLIER) cc_final: 0.8911 (tp30) outliers start: 111 outliers final: 73 residues processed: 316 average time/residue: 0.2713 time to fit residues: 141.5037 Evaluate side-chains 294 residues out of total 4120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 207 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 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 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 1007 PHE Chi-restraints excluded: chain Q residue 1017 PHE Chi-restraints excluded: chain Q residue 1089 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 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 132 ILE Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 435 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 247 ILE Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 215 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 463 LEU Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 388 THR Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 146 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 279 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.2949 > 50: distance: 64 - 69: 6.447 distance: 69 - 70: 11.295 distance: 70 - 71: 30.058 distance: 70 - 73: 25.543 distance: 71 - 72: 19.292 distance: 71 - 77: 23.353 distance: 73 - 74: 24.404 distance: 74 - 75: 20.503 distance: 74 - 76: 29.170 distance: 77 - 78: 16.851 distance: 78 - 79: 39.554 distance: 78 - 81: 25.856 distance: 79 - 80: 32.418 distance: 79 - 85: 19.630 distance: 81 - 82: 30.506 distance: 81 - 83: 17.837 distance: 82 - 84: 51.440 distance: 85 - 86: 28.601 distance: 86 - 87: 44.939 distance: 86 - 89: 25.431 distance: 87 - 88: 16.860 distance: 87 - 92: 20.342 distance: 89 - 90: 17.595 distance: 89 - 91: 23.928 distance: 92 - 93: 25.477 distance: 93 - 94: 9.599 distance: 93 - 96: 25.022 distance: 94 - 95: 37.002 distance: 94 - 103: 7.180 distance: 96 - 97: 14.125 distance: 97 - 98: 16.704 distance: 98 - 99: 9.339 distance: 99 - 100: 3.676 distance: 100 - 101: 8.460 distance: 100 - 102: 3.328 distance: 103 - 104: 17.615 distance: 104 - 105: 38.744 distance: 104 - 107: 33.446 distance: 105 - 106: 29.338 distance: 105 - 110: 41.311 distance: 107 - 108: 24.248 distance: 107 - 109: 14.062 distance: 110 - 111: 19.916 distance: 111 - 112: 14.247 distance: 111 - 114: 24.058 distance: 112 - 113: 10.277 distance: 112 - 118: 17.615 distance: 114 - 115: 14.373 distance: 115 - 116: 15.198 distance: 115 - 117: 43.613 distance: 118 - 119: 14.433 distance: 118 - 124: 49.217 distance: 119 - 120: 28.587 distance: 119 - 122: 28.584 distance: 120 - 121: 24.941 distance: 120 - 125: 27.522 distance: 122 - 123: 25.913 distance: 123 - 124: 14.310 distance: 125 - 126: 4.899 distance: 126 - 127: 15.951 distance: 126 - 129: 22.462 distance: 127 - 128: 16.579 distance: 127 - 137: 17.673 distance: 129 - 130: 13.969 distance: 130 - 131: 21.537 distance: 130 - 132: 22.939 distance: 131 - 133: 10.600 distance: 132 - 134: 10.994 distance: 133 - 135: 23.690 distance: 134 - 135: 27.794 distance: 135 - 136: 6.585 distance: 137 - 138: 11.056 distance: 138 - 139: 10.183 distance: 138 - 141: 7.982 distance: 139 - 140: 11.020 distance: 139 - 145: 14.522 distance: 140 - 171: 23.246 distance: 141 - 142: 10.664 distance: 142 - 143: 14.565 distance: 142 - 144: 3.076 distance: 145 - 146: 13.996 distance: 146 - 147: 27.535 distance: 146 - 149: 20.982 distance: 147 - 148: 12.222 distance: 147 - 154: 12.035 distance: 148 - 178: 13.334 distance: 149 - 150: 18.667 distance: 150 - 151: 8.915 distance: 151 - 152: 3.989 distance: 152 - 153: 24.143