Starting phenix.real_space_refine on Wed Aug 27 00:51:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9g_45361/08_2025/9c9g_45361_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9g_45361/08_2025/9c9g_45361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9g_45361/08_2025/9c9g_45361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9g_45361/08_2025/9c9g_45361.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9g_45361/08_2025/9c9g_45361_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9g_45361/08_2025/9c9g_45361_neut.cif" } resolution = 2.91 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= 0.001 sd= 0.034 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 300 5.49 5 S 107 5.16 5 C 26165 2.51 5 N 7616 2.21 5 O 8832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43020 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 722 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} 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: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 795 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: "Q" Number of atoms: 5289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5289 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 30, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4097 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 29, 'TRANS': 522} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 413 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 9, 'GLN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 9, 'ASN:plan1': 6, 'TYR:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 245 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: 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: "V" 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: "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: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3418 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 392 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2969 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.68, per 1000 atoms: 0.20 Number of scatterers: 43020 At special positions: 0 Unit cell: (130.26, 177.855, 218.77, 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 107 16.00 P 300 15.00 O 8832 8.00 N 7616 7.00 C 26165 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8938 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 41 sheets defined 49.1% alpha, 9.9% beta 129 base pairs and 232 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.515A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) 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 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.075A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.757A pdb=" N ILE D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 86 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.769A 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 removed outlier: 3.809A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 4.039A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.110A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.538A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.552A pdb=" N LYS G 21 " --> pdb=" O SER G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.463A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.532A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 removed outlier: 3.611A pdb=" N ASN G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 117 removed outlier: 3.504A pdb=" N LEU G 117 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.579A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 removed outlier: 4.017A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.577A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 Processing helix chain 'Q' and resid 709 through 724 removed outlier: 4.055A pdb=" N GLY Q 713 " --> pdb=" O TYR Q 709 " (cutoff:3.500A) Processing helix chain 'Q' and resid 736 through 752 Processing helix chain 'Q' and resid 766 through 778 Processing helix chain 'Q' and resid 789 through 800 Processing helix chain 'Q' and resid 819 through 826 removed outlier: 3.820A pdb=" N VAL Q 823 " --> pdb=" O SER Q 819 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 857 Processing helix chain 'Q' and resid 878 through 888 Processing helix chain 'Q' and resid 894 through 901 Processing helix chain 'Q' and resid 957 through 971 Processing helix chain 'Q' and resid 1004 through 1013 removed outlier: 3.617A pdb=" N VAL Q1010 " --> pdb=" O GLN Q1006 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.774A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE Q1094 " --> pdb=" O TYR Q1090 " (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 removed outlier: 3.586A pdb=" N THR Q1145 " --> pdb=" O PHE Q1141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1176 Processing helix chain 'Q' and resid 1177 through 1180 removed outlier: 4.155A pdb=" N ASN Q1180 " --> pdb=" O VAL Q1177 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1177 through 1180' Processing helix chain 'Q' and resid 1185 through 1190 Processing helix chain 'Q' and resid 1192 through 1201 removed outlier: 3.607A pdb=" N GLU Q1201 " --> pdb=" O ALA Q1197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.872A pdb=" N ILE Q1206 " --> pdb=" O LEU Q1203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 3.849A pdb=" N THR Q1230 " --> pdb=" O SER Q1226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1290 through 1297 Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 3.657A pdb=" N GLU Q1306 " --> pdb=" O ARG Q1302 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU Q1307 " --> pdb=" O LYS Q1303 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU Q1308 " --> pdb=" O LEU Q1304 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1330 through 1338 removed outlier: 3.597A pdb=" N TYR Q1334 " --> pdb=" O LEU Q1330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1352 through 1364 removed outlier: 3.842A pdb=" N ASP Q1356 " --> pdb=" O GLU Q1352 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL Q1358 " --> pdb=" O ARG Q1354 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS Q1359 " --> pdb=" O ARG Q1355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1397 through 1405 removed outlier: 3.515A pdb=" N GLN Q1403 " --> pdb=" O THR Q1399 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET Q1405 " --> pdb=" O ASP Q1401 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1446 removed outlier: 4.205A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL Q1445 " --> pdb=" O GLN Q1441 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 87 Processing helix chain 'R' and resid 89 through 95 Processing helix chain 'R' and resid 107 through 121 removed outlier: 4.079A pdb=" N THR R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 158 removed outlier: 3.514A pdb=" N ARG R 147 " --> pdb=" O VAL R 143 " (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 Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.801A pdb=" N ILE R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 456 Processing helix chain 'R' and resid 456 through 486 Processing helix chain 'R' and resid 490 through 503 Processing helix chain 'R' and resid 533 through 542 Processing helix chain 'R' and resid 545 through 570 removed outlier: 3.669A pdb=" N GLU R 550 " --> pdb=" O PRO R 546 " (cutoff:3.500A) Processing helix chain 'R' and resid 585 through 588 Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 607 through 609 No H-bonds generated for 'chain 'R' and resid 607 through 609' Processing helix chain 'R' and resid 616 through 621 removed outlier: 3.696A pdb=" N VAL R 621 " --> pdb=" O GLU R 617 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 626 removed outlier: 3.892A 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 647 Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 677 removed outlier: 3.570A pdb=" N ALA R 675 " --> pdb=" O GLY R 672 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 4.189A 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 730 through 738 Processing helix chain 'S' and resid 29 through 38 removed outlier: 3.848A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.965A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 151 through 157 Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.900A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 removed outlier: 3.640A pdb=" N GLY T 97 " --> pdb=" O SER T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.654A 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 257 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.748A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 removed outlier: 3.536A pdb=" N MET T 315 " --> pdb=" O GLU T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 328 removed outlier: 3.798A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.636A 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 removed outlier: 3.630A pdb=" N GLU T 391 " --> pdb=" O ARG T 387 " (cutoff:3.500A) Processing helix chain 'T' and resid 396 through 408 Processing helix chain 'T' and resid 411 through 418 removed outlier: 3.786A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.618A 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: 4.206A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 Processing helix chain 'U' and resid 241 through 249 Processing helix chain 'U' and resid 255 through 260 Processing helix chain 'U' and resid 267 through 283 removed outlier: 4.021A pdb=" N ASP U 271 " --> pdb=" O SER U 267 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN U 272 " --> pdb=" O GLU U 268 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE U 273 " --> pdb=" O VAL U 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 313 removed outlier: 3.807A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.749A 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: 3.623A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE U 403 " --> pdb=" O SER U 399 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.572A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'U' and resid 444 through 447 removed outlier: 3.597A 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: 3.909A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 removed outlier: 3.763A pdb=" N LEU V 88 " --> pdb=" O GLY V 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA V 89 " --> pdb=" O LYS V 85 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.779A 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 182 through 192 removed outlier: 3.613A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 270 Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.654A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 329 removed outlier: 3.633A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU V 329 " --> pdb=" O ASN V 325 " (cutoff:3.500A) 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 418 through 428 Processing helix chain 'V' and resid 435 through 446 removed outlier: 3.548A pdb=" N VAL V 439 " --> pdb=" O VAL V 435 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.556A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 92 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: 4.235A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.666A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.744A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.900A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.724A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 removed outlier: 3.585A pdb=" N ILE W 364 " --> pdb=" O ASN W 360 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.886A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG W 413 " --> pdb=" O ILE W 409 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 443 removed outlier: 3.568A pdb=" N ASN W 443 " --> pdb=" O TYR W 439 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.773A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 removed outlier: 3.538A pdb=" N GLY X 97 " --> pdb=" O SER X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.777A 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 184 No H-bonds generated for 'chain 'X' and resid 182 through 184' Processing helix chain 'X' and resid 185 through 192 Processing helix chain 'X' and resid 217 through 219 No H-bonds generated for 'chain 'X' and resid 217 through 219' Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.549A pdb=" N MET X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU X 272 " --> pdb=" O MET X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.714A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 328 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 Processing helix chain 'X' and resid 418 through 429 removed outlier: 3.673A pdb=" N SER X 429 " --> pdb=" O LEU X 425 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 Processing helix chain 'Y' and resid 47 through 64 removed outlier: 3.575A pdb=" N GLY Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 92 Processing helix chain 'Y' and resid 104 through 107 removed outlier: 3.802A pdb=" N PHE Y 107 " --> pdb=" O SER Y 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 107' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 207 through 209 No H-bonds generated for 'chain 'Y' and resid 207 through 209' Processing helix chain 'Y' and resid 241 through 248 Processing helix chain 'Y' and resid 253 through 260 Processing helix chain 'Y' and resid 266 through 284 removed outlier: 4.059A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 313 removed outlier: 3.502A pdb=" N LEU Y 313 " --> pdb=" O ILE Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 344 through 350 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: 4.167A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.587A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 442 Processing helix chain 'Y' and resid 443 through 447 removed outlier: 3.577A pdb=" N TYR Y 447 " --> pdb=" O GLU Y 444 " (cutoff:3.500A) Processing helix chain 'Z' and resid 250 through 277 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.187A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.769A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.939A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.783A pdb=" N THR F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.657A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.913A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (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: 7.528A 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 'G' and resid 43 through 44 removed outlier: 6.860A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'Q' and resid 783 through 784 removed outlier: 7.877A pdb=" N LEU Q 784 " --> pdb=" O VAL Q 817 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE Q 758 " --> pdb=" O MET Q 816 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR Q 818 " --> pdb=" O PHE Q 758 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL Q 760 " --> pdb=" O THR Q 818 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET Q 838 " --> pdb=" O LEU Q 866 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU Q 868 " --> pdb=" O MET Q 838 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU Q 840 " --> pdb=" O LEU Q 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 948 through 954 removed outlier: 3.566A pdb=" N CYS Q 954 " --> pdb=" O LEU Q1423 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL Q1389 " --> pdb=" O TYR Q1420 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU Q1422 " --> pdb=" O VAL Q1389 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE Q1391 " --> pdb=" O LEU Q1422 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N VAL Q1424 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE Q1343 " --> pdb=" O LEU Q1371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 6.245A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, 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 'V' and resid 163 through 172 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 175 through 181 current: chain 'V' and resid 209 through 215 removed outlier: 6.508A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.074A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 14 through 15 removed outlier: 6.620A pdb=" N VAL R 14 " --> pdb=" O GLU R 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 61 through 64 removed outlier: 3.883A pdb=" N THR R 137 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE R 44 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR R 164 " --> pdb=" O ILE R 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 67 through 68 Processing sheet with id=AB5, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.734A 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 removed outlier: 3.503A pdb=" N TYR S 125 " --> pdb=" O TYR S 134 " (cutoff:3.500A) 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: 6.271A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER T 340 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY T 79 " --> pdb=" O SER T 340 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 129 through 151 removed outlier: 6.176A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.383A 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: 6.620A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 6.135A 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 'T' and resid 394 through 395 removed outlier: 7.766A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AC5, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.235A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 125 through 147 removed outlier: 6.818A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 170 current: chain 'U' and resid 199 through 204 Processing sheet with id=AC7, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AC8, first strand: chain 'V' and resid 44 through 45 Processing sheet with id=AC9, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.414A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA V 339 " --> pdb=" O ILE V 310 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AD2, first strand: chain 'V' and resid 394 through 395 removed outlier: 7.485A pdb=" N GLN V 394 " --> pdb=" O ILE V 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AD4, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.387A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 125 through 147 removed outlier: 6.868A pdb=" N THR W 159 " --> pdb=" O VAL W 141 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE W 143 " --> pdb=" O LYS W 157 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS W 157 " --> pdb=" O ILE W 143 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE W 145 " --> pdb=" O GLN W 155 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN W 155 " --> pdb=" O ILE W 145 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU W 158 " --> pdb=" O TYR W 169 " (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 'X' and resid 162 through 172 removed outlier: 3.594A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.563A 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 211 through 215 removed outlier: 6.003A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 229 through 230 current: chain 'Z' and resid 315 through 318 Processing sheet with id=AD6, first strand: chain 'W' and resid 329 through 331 Processing sheet with id=AD7, first strand: chain 'X' and resid 44 through 45 Processing sheet with id=AD8, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.376A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER X 340 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AE1, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.836A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.539A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.402A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 125 through 147 removed outlier: 6.970A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 3.701A 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 205 removed outlier: 5.729A pdb=" N VAL Y 222 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG Y 204 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 329 through 331 1630 hydrogen bonds defined for protein. 4797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 232 stacking parallelities Total time for adding SS restraints: 12.56 Time building geometry restraints manager: 3.53 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: 11751 1.33 - 1.46: 11089 1.46 - 1.58: 20671 1.58 - 1.71: 594 1.71 - 1.83: 189 Bond restraints: 44294 Sorted by residual: bond pdb=" N SER Q1290 " pdb=" CA SER Q1290 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.31e+00 bond pdb=" N GLN C 105 " pdb=" CA GLN C 105 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.22e+00 bond pdb=" CB LYS D 82 " pdb=" CG LYS D 82 " ideal model delta sigma weight residual 1.520 1.593 -0.073 3.00e-02 1.11e+03 5.89e+00 bond pdb=" CA SER Q1287 " pdb=" CB SER Q1287 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.82e-02 3.02e+03 5.35e+00 bond pdb=" CB PHE H 73 " pdb=" CG PHE H 73 " ideal model delta sigma weight residual 1.502 1.555 -0.053 2.30e-02 1.89e+03 5.21e+00 ... (remaining 44289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 60573 3.99 - 7.98: 466 7.98 - 11.97: 107 11.97 - 15.96: 18 15.96 - 19.95: 12 Bond angle restraints: 61176 Sorted by residual: angle pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " pdb=" CG GLU F 63 " ideal model delta sigma weight residual 114.10 127.90 -13.80 2.00e+00 2.50e-01 4.76e+01 angle pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " pdb=" CG GLU A 105 " ideal model delta sigma weight residual 114.10 126.82 -12.72 2.00e+00 2.50e-01 4.04e+01 angle pdb=" CA LYS D 82 " pdb=" CB LYS D 82 " pdb=" CG LYS D 82 " ideal model delta sigma weight residual 114.10 126.74 -12.64 2.00e+00 2.50e-01 3.99e+01 angle pdb=" CB LYS U 94 " pdb=" CG LYS U 94 " pdb=" CD LYS U 94 " ideal model delta sigma weight residual 111.30 124.93 -13.63 2.30e+00 1.89e-01 3.51e+01 angle pdb=" CA LYS A 42 " pdb=" CB LYS A 42 " pdb=" CG LYS A 42 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 ... (remaining 61171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 24054 35.19 - 70.39: 2106 70.39 - 105.58: 62 105.58 - 140.78: 4 140.78 - 175.97: 5 Dihedral angle restraints: 26231 sinusoidal: 12403 harmonic: 13828 Sorted by residual: dihedral pdb=" O2A ADP W 501 " pdb=" O3A ADP W 501 " pdb=" PA ADP W 501 " pdb=" PB ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 85.18 -145.18 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP W 501 " pdb=" O3A ADP W 501 " pdb=" PB ADP W 501 " pdb=" PA ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 81.54 -141.54 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" C5' ADP U 501 " pdb=" O5' ADP U 501 " pdb=" PA ADP U 501 " pdb=" O2A ADP U 501 " ideal model delta sinusoidal sigma weight residual -60.00 -176.59 116.59 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 26228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 6637 0.100 - 0.201: 455 0.201 - 0.301: 23 0.301 - 0.402: 4 0.402 - 0.502: 1 Chirality restraints: 7120 Sorted by residual: chirality pdb=" CG LEU C 86 " pdb=" CB LEU C 86 " pdb=" CD1 LEU C 86 " pdb=" CD2 LEU C 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB VAL H 47 " pdb=" CA VAL H 47 " pdb=" CG1 VAL H 47 " pdb=" CG2 VAL H 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CG LEU H 65 " pdb=" CB LEU H 65 " pdb=" CD1 LEU H 65 " pdb=" CD2 LEU H 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 7117 not shown) Planarity restraints: 6821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 770 " -0.027 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP Q 770 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 770 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 770 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 770 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 770 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 770 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 770 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 770 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 770 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 68 " 0.020 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE D 68 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE D 68 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE D 68 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 68 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 68 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 68 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 74 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" CD GLU D 74 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLU D 74 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU D 74 " 0.020 2.00e-02 2.50e+03 ... (remaining 6818 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 17 2.30 - 2.95: 17962 2.95 - 3.60: 64021 3.60 - 4.25: 101073 4.25 - 4.90: 163776 Nonbonded interactions: 346849 Sorted by model distance: nonbonded pdb=" NH1 ARG G 30 " pdb=" OE1 GLU H 38 " model vdw 1.653 3.120 nonbonded pdb=" OG1 THR V 86 " pdb=" O1A ADP V 501 " model vdw 1.994 3.040 nonbonded pdb=" NH1 ARG G 89 " pdb=" OD1 ASN G 95 " model vdw 2.048 3.120 nonbonded pdb=" OD1 ASN R 615 " pdb=" N VAL R 616 " model vdw 2.055 3.120 nonbonded pdb=" NH1 ARG G 30 " pdb=" CD GLU H 38 " model vdw 2.174 3.350 ... (remaining 346844 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 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 102)) selection = (chain 'F' and (resid 24 through 84 or (resid 85 and (name N or name CA or name \ C or name O or name CB )) or resid 86 through 102)) } 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 118)) selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 36 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 128)) } ncs_group { reference = (chain 'T' and resid 22 through 501) 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 501)) 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 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 181 or (resid 182 and (name N o \ r name CA or name C or name O or name CB )) or resid 183 through 210 or resid 22 \ 1 through 501)) selection = (chain 'Y' 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 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.460 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 41.450 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 : 0.006 0.088 44296 Z= 0.250 Angle : 0.988 19.951 61176 Z= 0.502 Chirality : 0.052 0.502 7120 Planarity : 0.006 0.076 6821 Dihedral : 21.611 175.973 17293 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 29.54 % Favored : 70.46 % 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 aren not related in a simple way. whole: -1.90 (0.11), residues: 4723 helix: -1.41 (0.09), residues: 2255 sheet: 0.48 (0.21), residues: 662 loop : -1.55 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 95 TYR 0.050 0.002 TYR D 43 PHE 0.060 0.002 PHE D 68 TRP 0.063 0.004 TRP Q 770 HIS 0.008 0.001 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00577 (44294) covalent geometry : angle 0.98785 (61176) hydrogen bonds : bond 0.16204 ( 1956) hydrogen bonds : angle 6.34654 ( 5449) Misc. bond : bond 0.00203 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.522 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: A 105 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8931 (mp0) REVERT: C 39 ASN cc_start: 0.9105 (p0) cc_final: 0.8898 (p0) REVERT: G 73 ASP cc_start: 0.8883 (t0) cc_final: 0.8678 (t0) REVERT: H 49 LYS cc_start: 0.9039 (tppt) cc_final: 0.8498 (tppp) REVERT: Q 716 TRP cc_start: 0.4645 (t60) cc_final: 0.3989 (t-100) REVERT: Q 926 MET cc_start: 0.8144 (mmt) cc_final: 0.7873 (pmm) REVERT: Q 1324 MET cc_start: 0.7574 (mpp) cc_final: 0.6733 (mtt) REVERT: U 86 MET cc_start: 0.9181 (mmm) cc_final: 0.8668 (tpp) REVERT: U 94 LYS cc_start: 0.8866 (tppt) cc_final: 0.8448 (tptp) REVERT: V 315 MET cc_start: 0.9384 (mmm) cc_final: 0.9163 (mmp) REVERT: F 27 GLN cc_start: 0.9262 (mp10) cc_final: 0.8408 (mp10) REVERT: F 55 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7407 (mtt180) REVERT: F 93 GLN cc_start: 0.8981 (mt0) cc_final: 0.8674 (tm-30) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.7693 time to fit residues: 280.7724 Evaluate side-chains 267 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 494 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 115 ASN D 66 ASN G 42 GLN G 90 ASN Q 875 ASN Q1204 ASN R 146 GLN V 298 GLN V 440 ASN X 51 GLN Y 23 HIS F 64 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.077101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048450 restraints weight = 156386.401| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.02 r_work: 0.2790 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44296 Z= 0.146 Angle : 0.607 11.957 61176 Z= 0.318 Chirality : 0.041 0.267 7120 Planarity : 0.004 0.046 6821 Dihedral : 21.601 177.195 8363 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.65 % Allowed : 25.86 % Favored : 71.49 % 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 aren not related in a simple way. whole: -0.48 (0.12), residues: 4723 helix: 0.22 (0.11), residues: 2267 sheet: 0.52 (0.20), residues: 669 loop : -1.26 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 95 TYR 0.022 0.001 TYR V 462 PHE 0.022 0.001 PHE R 691 TRP 0.023 0.002 TRP Q 716 HIS 0.005 0.001 HIS Q1316 Details of bonding type rmsd covalent geometry : bond 0.00325 (44294) covalent geometry : angle 0.60683 (61176) hydrogen bonds : bond 0.04381 ( 1956) hydrogen bonds : angle 4.02700 ( 5449) Misc. bond : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 280 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 GLN cc_start: 0.8803 (pm20) cc_final: 0.8452 (pm20) REVERT: D 88 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9224 (mmpt) REVERT: D 89 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8168 (ttpt) REVERT: E 76 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8522 (tp-100) REVERT: G 58 TYR cc_start: 0.8831 (t80) cc_final: 0.8596 (t80) REVERT: G 90 ASN cc_start: 0.9198 (t0) cc_final: 0.8900 (t0) REVERT: H 45 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8857 (t80) REVERT: H 49 LYS cc_start: 0.8869 (tppt) cc_final: 0.8600 (tppp) REVERT: H 116 GLU cc_start: 0.8850 (tt0) cc_final: 0.8388 (tm-30) REVERT: Q 926 MET cc_start: 0.8454 (mmt) cc_final: 0.8139 (pmm) REVERT: Q 1406 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8219 (t0) REVERT: R 714 MET cc_start: 0.9103 (mmm) cc_final: 0.8845 (mtt) REVERT: U 86 MET cc_start: 0.9159 (mmm) cc_final: 0.8652 (tpp) REVERT: W 86 MET cc_start: 0.8768 (tpp) cc_final: 0.8550 (tpp) REVERT: W 212 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7171 (p90) REVERT: X 258 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8186 (tmm-80) REVERT: Y 23 HIS cc_start: 0.9377 (OUTLIER) cc_final: 0.8884 (p-80) REVERT: Y 279 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8480 (pp20) REVERT: F 27 GLN cc_start: 0.9317 (mp10) cc_final: 0.8604 (mp10) REVERT: F 84 MET cc_start: 0.7313 (tmm) cc_final: 0.6803 (tmm) REVERT: F 93 GLN cc_start: 0.9102 (mt0) cc_final: 0.8748 (tm-30) REVERT: F 100 PHE cc_start: 0.8654 (m-10) cc_final: 0.8349 (m-10) outliers start: 105 outliers final: 23 residues processed: 359 average time/residue: 0.7356 time to fit residues: 320.9881 Evaluate side-chains 287 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1406 ASP Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 331 ASN Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain V residue 234 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 187 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 468 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 0.0670 chunk 256 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN W 155 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.076826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048208 restraints weight = 156316.966| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.99 r_work: 0.2785 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44296 Z= 0.143 Angle : 0.587 11.726 61176 Z= 0.304 Chirality : 0.040 0.391 7120 Planarity : 0.003 0.047 6821 Dihedral : 21.501 175.774 8363 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.90 % Allowed : 25.16 % Favored : 71.94 % 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 aren not related in a simple way. whole: 0.09 (0.12), residues: 4723 helix: 0.88 (0.11), residues: 2270 sheet: 0.49 (0.20), residues: 698 loop : -1.16 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.019 0.001 TYR V 462 PHE 0.021 0.001 PHE R 691 TRP 0.022 0.001 TRP Q 770 HIS 0.017 0.001 HIS Y 23 Details of bonding type rmsd covalent geometry : bond 0.00328 (44294) covalent geometry : angle 0.58664 (61176) hydrogen bonds : bond 0.03949 ( 1956) hydrogen bonds : angle 3.77638 ( 5449) Misc. bond : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 280 time to evaluate : 1.773 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: C 114 GLN cc_start: 0.8872 (pm20) cc_final: 0.8485 (pm20) REVERT: D 89 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8179 (ttpt) REVERT: D 123 LYS cc_start: 0.9496 (tptm) cc_final: 0.9279 (tppt) REVERT: E 76 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8502 (tp-100) REVERT: E 97 GLU cc_start: 0.8598 (pp20) cc_final: 0.8336 (pp20) REVERT: G 73 ASP cc_start: 0.9134 (t0) cc_final: 0.8884 (t0) REVERT: G 90 ASN cc_start: 0.9237 (t0) cc_final: 0.8902 (t0) REVERT: H 45 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8874 (t80) REVERT: H 46 LYS cc_start: 0.9362 (mtmm) cc_final: 0.9142 (mtmm) REVERT: H 49 LYS cc_start: 0.8859 (tppt) cc_final: 0.8562 (tppp) REVERT: H 116 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: Q 846 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7233 (tp) REVERT: Q 926 MET cc_start: 0.8464 (mmt) cc_final: 0.8145 (pmm) REVERT: Q 1324 MET cc_start: 0.7539 (mpp) cc_final: 0.6627 (mtt) REVERT: Q 1372 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7536 (tp) REVERT: T 125 PHE cc_start: 0.9495 (OUTLIER) cc_final: 0.9185 (t80) REVERT: W 212 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7054 (p90) REVERT: X 211 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8190 (ttt90) REVERT: X 258 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8167 (tmm-80) REVERT: Y 279 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8489 (pp20) REVERT: F 67 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8374 (ttm110) REVERT: F 84 MET cc_start: 0.7051 (tmm) cc_final: 0.6478 (tmm) REVERT: F 93 GLN cc_start: 0.9073 (mt0) cc_final: 0.8736 (tm-30) outliers start: 115 outliers final: 34 residues processed: 367 average time/residue: 0.7022 time to fit residues: 315.4899 Evaluate side-chains 304 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 846 ILE Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1372 LEU Chi-restraints excluded: chain Q residue 1406 ASP Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 731 LYS Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain V residue 234 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 211 ARG Chi-restraints excluded: chain X residue 350 THR Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 454 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 431 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 497 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1359 HIS ** Q1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN V 190 GLN V 437 ASN Y 23 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.075292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046637 restraints weight = 157600.743| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.97 r_work: 0.2742 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 44296 Z= 0.221 Angle : 0.623 11.115 61176 Z= 0.323 Chirality : 0.042 0.242 7120 Planarity : 0.004 0.049 6821 Dihedral : 21.593 176.856 8363 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.18 % Allowed : 25.03 % Favored : 71.79 % 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 aren not related in a simple way. whole: 0.29 (0.12), residues: 4723 helix: 1.13 (0.11), residues: 2281 sheet: 0.47 (0.20), residues: 688 loop : -1.14 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 72 TYR 0.025 0.001 TYR V 462 PHE 0.020 0.001 PHE R 691 TRP 0.024 0.002 TRP Q 770 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00511 (44294) covalent geometry : angle 0.62273 (61176) hydrogen bonds : bond 0.04746 ( 1956) hydrogen bonds : angle 3.83020 ( 5449) Misc. bond : bond 0.00139 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 275 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 ARG cc_start: 0.8720 (mpt180) cc_final: 0.8324 (mtm-85) REVERT: C 114 GLN cc_start: 0.8892 (pm20) cc_final: 0.8559 (pm20) REVERT: D 123 LYS cc_start: 0.9478 (tptm) cc_final: 0.9264 (tppt) REVERT: E 76 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8453 (tp-100) REVERT: G 18 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7546 (mtt180) REVERT: G 58 TYR cc_start: 0.8929 (t80) cc_final: 0.8691 (t80) REVERT: G 76 LYS cc_start: 0.7916 (tmtt) cc_final: 0.7704 (tptm) REVERT: G 90 ASN cc_start: 0.9294 (t0) cc_final: 0.8936 (t0) REVERT: G 91 ASP cc_start: 0.8257 (t70) cc_final: 0.7794 (t0) REVERT: G 100 ASN cc_start: 0.9107 (t0) cc_final: 0.8480 (t0) REVERT: H 45 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8882 (t80) REVERT: H 46 LYS cc_start: 0.9388 (mtmm) cc_final: 0.8978 (mtmm) REVERT: H 49 LYS cc_start: 0.8808 (tppt) cc_final: 0.8459 (tppp) REVERT: H 96 GLU cc_start: 0.8980 (mp0) cc_final: 0.8403 (mp0) REVERT: H 116 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: Q 846 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7370 (tp) REVERT: Q 926 MET cc_start: 0.8487 (mmt) cc_final: 0.8168 (pmm) REVERT: Q 1180 ASN cc_start: 0.8972 (m-40) cc_final: 0.8719 (t0) REVERT: Q 1183 SER cc_start: 0.8600 (t) cc_final: 0.8169 (p) REVERT: Q 1372 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7639 (tp) REVERT: R 719 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8241 (mtm-85) REVERT: T 269 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7414 (mpt) REVERT: U 86 MET cc_start: 0.9192 (mmm) cc_final: 0.8762 (tpp) REVERT: W 86 MET cc_start: 0.8797 (tpp) cc_final: 0.8588 (tpp) REVERT: W 212 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7026 (p90) REVERT: X 258 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8161 (tmm-80) REVERT: Y 23 HIS cc_start: 0.9317 (OUTLIER) cc_final: 0.8707 (p-80) REVERT: F 67 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8251 (ttm110) REVERT: F 93 GLN cc_start: 0.9035 (mt0) cc_final: 0.8746 (tm-30) outliers start: 126 outliers final: 40 residues processed: 373 average time/residue: 0.7313 time to fit residues: 333.3526 Evaluate side-chains 310 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 735 LEU Chi-restraints excluded: chain Q residue 846 ILE Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 880 LEU Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1372 LEU Chi-restraints excluded: chain Q residue 1406 ASP Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 331 ASN Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 350 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 178 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 328 optimal weight: 0.7980 chunk 410 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 338 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 226 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN E 85 GLN G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1416 GLN R 146 GLN Y 23 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.076083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047504 restraints weight = 157551.536| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.00 r_work: 0.2771 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44296 Z= 0.140 Angle : 0.589 11.640 61176 Z= 0.304 Chirality : 0.040 0.221 7120 Planarity : 0.003 0.049 6821 Dihedral : 21.555 176.262 8363 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.82 % Allowed : 25.91 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.12), residues: 4723 helix: 1.31 (0.11), residues: 2283 sheet: 0.42 (0.20), residues: 704 loop : -1.04 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 72 TYR 0.017 0.001 TYR V 462 PHE 0.020 0.001 PHE R 691 TRP 0.024 0.001 TRP Q 770 HIS 0.013 0.001 HIS Y 23 Details of bonding type rmsd covalent geometry : bond 0.00321 (44294) covalent geometry : angle 0.58874 (61176) hydrogen bonds : bond 0.03790 ( 1956) hydrogen bonds : angle 3.63800 ( 5449) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 280 time to evaluate : 1.494 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: A 58 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8730 (m) REVERT: A 64 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9116 (mmtm) REVERT: C 18 ARG cc_start: 0.9381 (mtp-110) cc_final: 0.8878 (mtp-110) REVERT: C 37 ARG cc_start: 0.8738 (mpt180) cc_final: 0.8347 (mtm-85) REVERT: C 66 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9189 (mm) REVERT: C 114 GLN cc_start: 0.8865 (pm20) cc_final: 0.8526 (pm20) REVERT: E 50 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8723 (pm20) REVERT: E 64 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9146 (mmmm) REVERT: E 76 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8417 (tp-100) REVERT: E 85 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: G 58 TYR cc_start: 0.8920 (t80) cc_final: 0.8681 (t80) REVERT: G 76 LYS cc_start: 0.7792 (tmtt) cc_final: 0.7559 (tptm) REVERT: G 90 ASN cc_start: 0.9285 (t0) cc_final: 0.8924 (t0) REVERT: G 100 ASN cc_start: 0.9126 (t0) cc_final: 0.8415 (t0) REVERT: H 45 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8863 (t80) REVERT: H 46 LYS cc_start: 0.9353 (mtmm) cc_final: 0.9117 (mtmm) REVERT: H 49 LYS cc_start: 0.8755 (tppt) cc_final: 0.8395 (tppp) REVERT: H 96 GLU cc_start: 0.8977 (mp0) cc_final: 0.8401 (mp0) REVERT: H 116 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8379 (tm-30) REVERT: Q 846 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7301 (tp) REVERT: Q 926 MET cc_start: 0.8477 (mmt) cc_final: 0.8154 (pmm) REVERT: Q 1016 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7313 (mm) REVERT: Q 1183 SER cc_start: 0.8578 (t) cc_final: 0.8145 (p) REVERT: Q 1324 MET cc_start: 0.7461 (mpp) cc_final: 0.6658 (mtt) REVERT: Q 1372 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7577 (tp) REVERT: T 125 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9146 (t80) REVERT: T 269 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7245 (mpt) REVERT: U 86 MET cc_start: 0.9167 (mmm) cc_final: 0.8690 (tpp) REVERT: W 86 MET cc_start: 0.8774 (tpp) cc_final: 0.8572 (tpp) REVERT: W 212 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.6909 (p90) REVERT: X 258 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8091 (tmm-80) REVERT: Y 23 HIS cc_start: 0.9292 (OUTLIER) cc_final: 0.9022 (p-80) REVERT: B 74 GLU cc_start: 0.9411 (tp30) cc_final: 0.9133 (pt0) REVERT: F 67 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8361 (ttp-110) REVERT: F 93 GLN cc_start: 0.9026 (mt0) cc_final: 0.8741 (tm-30) outliers start: 112 outliers final: 45 residues processed: 368 average time/residue: 0.7095 time to fit residues: 319.4912 Evaluate side-chains 320 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 735 LEU Chi-restraints excluded: chain Q residue 846 ILE Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1016 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1372 LEU Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 331 ASN Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain T residue 428 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 174 LYS Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 450 ASP Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 386 optimal weight: 0.9990 chunk 340 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 412 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN D 66 ASN G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN Y 23 HIS ** B 25 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 = 0.3730 r_free = 0.3730 target = 0.075478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046928 restraints weight = 157818.120| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.97 r_work: 0.2752 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 44296 Z= 0.178 Angle : 0.610 12.884 61176 Z= 0.313 Chirality : 0.041 0.389 7120 Planarity : 0.003 0.050 6821 Dihedral : 21.573 179.937 8363 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.70 % Allowed : 26.34 % Favored : 70.96 % 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 aren not related in a simple way. whole: 0.53 (0.13), residues: 4723 helix: 1.39 (0.11), residues: 2283 sheet: 0.43 (0.20), residues: 697 loop : -1.05 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 72 TYR 0.020 0.001 TYR V 462 PHE 0.020 0.001 PHE R 691 TRP 0.026 0.001 TRP Q 770 HIS 0.007 0.001 HIS Y 23 Details of bonding type rmsd covalent geometry : bond 0.00415 (44294) covalent geometry : angle 0.61043 (61176) hydrogen bonds : bond 0.04105 ( 1956) hydrogen bonds : angle 3.65738 ( 5449) Misc. bond : bond 0.00116 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 277 time to evaluate : 1.592 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: A 58 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8740 (m) REVERT: A 64 LYS cc_start: 0.9583 (mmmm) cc_final: 0.9150 (mmtm) REVERT: A 105 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8995 (mm-30) REVERT: C 18 ARG cc_start: 0.9396 (mtp-110) cc_final: 0.8882 (mtp-110) REVERT: C 37 ARG cc_start: 0.8748 (mpt180) cc_final: 0.8396 (mtm-85) REVERT: C 69 ASN cc_start: 0.9644 (m-40) cc_final: 0.9395 (p0) REVERT: C 114 GLN cc_start: 0.8883 (pm20) cc_final: 0.8526 (pm20) REVERT: E 64 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9146 (mmmm) REVERT: E 76 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8423 (tp-100) REVERT: G 90 ASN cc_start: 0.9310 (t0) cc_final: 0.8951 (t0) REVERT: G 100 ASN cc_start: 0.9133 (t0) cc_final: 0.8765 (t0) REVERT: H 45 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8852 (t80) REVERT: H 46 LYS cc_start: 0.9381 (mtmm) cc_final: 0.9098 (mtmm) REVERT: H 49 LYS cc_start: 0.8720 (tppt) cc_final: 0.8343 (tppp) REVERT: H 96 GLU cc_start: 0.8974 (mp0) cc_final: 0.8395 (mp0) REVERT: H 116 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: Q 846 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7444 (tp) REVERT: Q 926 MET cc_start: 0.8478 (mmt) cc_final: 0.8161 (pmm) REVERT: Q 1016 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7389 (mm) REVERT: Q 1180 ASN cc_start: 0.8896 (m-40) cc_final: 0.8664 (t0) REVERT: Q 1324 MET cc_start: 0.7467 (mpp) cc_final: 0.6732 (mtt) REVERT: Q 1372 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7590 (tp) REVERT: T 125 PHE cc_start: 0.9507 (OUTLIER) cc_final: 0.9117 (t80) REVERT: T 269 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7229 (mpt) REVERT: U 86 MET cc_start: 0.9173 (mmm) cc_final: 0.8748 (tpp) REVERT: U 142 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7970 (tm-30) REVERT: U 144 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8254 (mt0) REVERT: W 212 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6850 (p90) REVERT: X 222 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7745 (t80) REVERT: X 258 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8087 (tmm-80) REVERT: Y 23 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.8914 (p-80) REVERT: F 40 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8217 (mmp-170) REVERT: F 55 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7552 (mtt180) REVERT: F 67 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8309 (ttp-110) REVERT: F 93 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8774 (tm-30) outliers start: 107 outliers final: 46 residues processed: 360 average time/residue: 0.7004 time to fit residues: 308.0171 Evaluate side-chains 322 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 735 LEU Chi-restraints excluded: chain Q residue 846 ILE Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1016 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1372 LEU Chi-restraints excluded: chain Q residue 1406 ASP Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 428 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 174 LYS Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain X residue 350 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 450 ASP Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 240 optimal weight: 0.0470 chunk 27 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 289 optimal weight: 0.0980 chunk 381 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 437 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 429 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN D 66 ASN G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN X 245 GLN ** B 25 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 = 0.3755 r_free = 0.3755 target = 0.076731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048320 restraints weight = 156590.987| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.00 r_work: 0.2789 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44296 Z= 0.117 Angle : 0.601 12.487 61176 Z= 0.306 Chirality : 0.040 0.449 7120 Planarity : 0.003 0.049 6821 Dihedral : 21.473 177.526 8363 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.17 % Allowed : 27.00 % Favored : 70.83 % 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 aren not related in a simple way. whole: 0.68 (0.13), residues: 4723 helix: 1.49 (0.11), residues: 2286 sheet: 0.58 (0.20), residues: 674 loop : -0.97 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 72 TYR 0.020 0.001 TYR C 40 PHE 0.019 0.001 PHE R 691 TRP 0.030 0.001 TRP Q 770 HIS 0.013 0.001 HIS Y 23 Details of bonding type rmsd covalent geometry : bond 0.00263 (44294) covalent geometry : angle 0.60095 (61176) hydrogen bonds : bond 0.03339 ( 1956) hydrogen bonds : angle 3.48560 ( 5449) Misc. bond : bond 0.00101 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 1.274 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: A 56 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8146 (mmtt) REVERT: A 64 LYS cc_start: 0.9562 (mmmm) cc_final: 0.9134 (mmtm) REVERT: A 105 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8908 (mm-30) REVERT: A 106 ASP cc_start: 0.9007 (p0) cc_final: 0.8741 (p0) REVERT: C 18 ARG cc_start: 0.9430 (mtp-110) cc_final: 0.8971 (mtp-110) REVERT: C 69 ASN cc_start: 0.9630 (m-40) cc_final: 0.9389 (p0) REVERT: C 96 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8417 (pmtt) REVERT: C 114 GLN cc_start: 0.8856 (pm20) cc_final: 0.8492 (pm20) REVERT: C 115 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7853 (t0) REVERT: D 96 GLU cc_start: 0.8949 (mp0) cc_final: 0.8737 (mp0) REVERT: E 76 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8411 (tp-100) REVERT: G 90 ASN cc_start: 0.9304 (t0) cc_final: 0.8950 (t0) REVERT: H 96 GLU cc_start: 0.8974 (mp0) cc_final: 0.8400 (mp0) REVERT: H 116 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: Q 846 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7375 (tp) REVERT: Q 926 MET cc_start: 0.8509 (mmt) cc_final: 0.8210 (pmm) REVERT: Q 1016 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7089 (mm) REVERT: Q 1183 SER cc_start: 0.8554 (t) cc_final: 0.8125 (p) REVERT: Q 1324 MET cc_start: 0.7391 (mpp) cc_final: 0.6658 (mtt) REVERT: T 269 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7144 (mpt) REVERT: U 86 MET cc_start: 0.9137 (mmm) cc_final: 0.8643 (tpp) REVERT: U 166 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8495 (tp30) REVERT: W 212 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.6791 (p90) REVERT: X 222 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7678 (t80) REVERT: X 258 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8229 (tmm-80) REVERT: Y 23 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8456 (p90) REVERT: Y 279 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8503 (pp20) REVERT: B 74 GLU cc_start: 0.9551 (tp30) cc_final: 0.9185 (pt0) REVERT: F 40 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8041 (mmp-170) REVERT: F 67 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8259 (ttp-110) REVERT: F 93 GLN cc_start: 0.9064 (mt0) cc_final: 0.8781 (tm-30) outliers start: 86 outliers final: 35 residues processed: 349 average time/residue: 0.7289 time to fit residues: 308.9169 Evaluate side-chains 309 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 846 ILE Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 1016 LEU Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1406 ASP Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 185 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 450 ASP Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 8.9990 chunk 179 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 272 optimal weight: 0.2980 chunk 362 optimal weight: 0.4980 chunk 117 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN D 66 ASN G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.075691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047203 restraints weight = 158190.668| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.00 r_work: 0.2758 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 44296 Z= 0.166 Angle : 0.630 13.540 61176 Z= 0.318 Chirality : 0.041 0.395 7120 Planarity : 0.003 0.061 6821 Dihedral : 21.507 177.302 8363 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.14 % Allowed : 27.58 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.13), residues: 4723 helix: 1.54 (0.11), residues: 2280 sheet: 0.47 (0.20), residues: 693 loop : -0.95 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 72 TYR 0.019 0.001 TYR C 40 PHE 0.023 0.001 PHE H 73 TRP 0.024 0.001 TRP Q1396 HIS 0.007 0.001 HIS Y 23 Details of bonding type rmsd covalent geometry : bond 0.00388 (44294) covalent geometry : angle 0.63009 (61176) hydrogen bonds : bond 0.03980 ( 1956) hydrogen bonds : angle 3.55753 ( 5449) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 270 time to evaluate : 1.230 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: A 64 LYS cc_start: 0.9572 (mmmm) cc_final: 0.9150 (mmtm) REVERT: A 105 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8945 (mm-30) REVERT: C 18 ARG cc_start: 0.9445 (mtp-110) cc_final: 0.8945 (mtp-110) REVERT: C 37 ARG cc_start: 0.8709 (mpt180) cc_final: 0.8311 (mtm-85) REVERT: C 69 ASN cc_start: 0.9641 (m-40) cc_final: 0.9403 (p0) REVERT: D 88 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9195 (mmpt) REVERT: E 76 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8380 (tp-100) REVERT: E 97 GLU cc_start: 0.8646 (pp20) cc_final: 0.8433 (pp20) REVERT: G 90 ASN cc_start: 0.9317 (t0) cc_final: 0.8959 (t0) REVERT: H 96 GLU cc_start: 0.8989 (mp0) cc_final: 0.8411 (mp0) REVERT: H 116 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: Q 846 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7362 (tp) REVERT: Q 926 MET cc_start: 0.8493 (mmt) cc_final: 0.8184 (pmm) REVERT: Q 1180 ASN cc_start: 0.8916 (m-40) cc_final: 0.8689 (t0) REVERT: T 269 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7207 (mpt) REVERT: U 86 MET cc_start: 0.9155 (mmm) cc_final: 0.8716 (tpp) REVERT: U 144 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8356 (mt0) REVERT: W 212 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6790 (p90) REVERT: X 222 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7688 (t80) REVERT: X 258 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8241 (tmm-80) REVERT: Y 23 HIS cc_start: 0.9285 (OUTLIER) cc_final: 0.8747 (p90) REVERT: F 55 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7555 (mtt180) REVERT: F 93 GLN cc_start: 0.9088 (mt0) cc_final: 0.8779 (tm-30) outliers start: 85 outliers final: 42 residues processed: 335 average time/residue: 0.7010 time to fit residues: 287.3040 Evaluate side-chains 310 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 846 ILE Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1406 ASP Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 428 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 185 LEU Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 450 ASP Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 263 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 419 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 395 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 474 optimal weight: 7.9990 chunk 493 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.074774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047069 restraints weight = 155863.232| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.06 r_work: 0.2722 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 44296 Z= 0.219 Angle : 0.679 15.018 61176 Z= 0.342 Chirality : 0.042 0.375 7120 Planarity : 0.003 0.067 6821 Dihedral : 21.643 177.803 8363 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.17 % Allowed : 27.58 % Favored : 70.25 % 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 aren not related in a simple way. whole: 0.64 (0.13), residues: 4723 helix: 1.51 (0.11), residues: 2278 sheet: 0.43 (0.20), residues: 692 loop : -1.01 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 72 TYR 0.024 0.001 TYR V 462 PHE 0.020 0.001 PHE R 691 TRP 0.035 0.002 TRP Q1396 HIS 0.007 0.001 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00512 (44294) covalent geometry : angle 0.67855 (61176) hydrogen bonds : bond 0.04594 ( 1956) hydrogen bonds : angle 3.72151 ( 5449) Misc. bond : bond 0.00145 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 274 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8123 (mmmt) REVERT: A 59 GLU cc_start: 0.9276 (tp30) cc_final: 0.8994 (mp0) REVERT: A 64 LYS cc_start: 0.9606 (mmmm) cc_final: 0.9211 (mmtm) REVERT: A 105 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8924 (mm-30) REVERT: C 37 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8342 (mtm-85) REVERT: C 69 ASN cc_start: 0.9645 (m-40) cc_final: 0.9418 (p0) REVERT: C 114 GLN cc_start: 0.8836 (pm20) cc_final: 0.8528 (pm20) REVERT: D 88 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9194 (mmpt) REVERT: E 76 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8369 (tp-100) REVERT: G 90 ASN cc_start: 0.9373 (t0) cc_final: 0.9024 (t0) REVERT: H 82 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8944 (tptt) REVERT: H 96 GLU cc_start: 0.9031 (mp0) cc_final: 0.8442 (mp0) REVERT: H 116 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8445 (tm-30) REVERT: Q 926 MET cc_start: 0.8436 (mmt) cc_final: 0.8146 (pmm) REVERT: Q 1316 HIS cc_start: 0.6613 (OUTLIER) cc_final: 0.6388 (t70) REVERT: Q 1324 MET cc_start: 0.7572 (mpp) cc_final: 0.7082 (mtt) REVERT: Q 1331 MET cc_start: 0.8605 (mmm) cc_final: 0.8362 (mmm) REVERT: Q 1355 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7418 (ttp-170) REVERT: Q 1372 LEU cc_start: 0.8463 (mt) cc_final: 0.7926 (tp) REVERT: R 28 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8526 (p90) REVERT: R 719 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8304 (mtm-85) REVERT: T 269 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7217 (mpt) REVERT: U 86 MET cc_start: 0.9230 (mmm) cc_final: 0.8800 (tpp) REVERT: W 212 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6818 (p90) REVERT: X 221 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: X 222 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7672 (t80) REVERT: Y 23 HIS cc_start: 0.9333 (OUTLIER) cc_final: 0.8700 (p90) REVERT: F 40 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7816 (mmp-170) REVERT: F 93 GLN cc_start: 0.9125 (mt0) cc_final: 0.8797 (tm-30) outliers start: 86 outliers final: 39 residues processed: 341 average time/residue: 0.7130 time to fit residues: 298.8175 Evaluate side-chains 307 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 428 THR Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 221 GLU Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 450 ASP Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 17 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 chunk 283 optimal weight: 0.0670 chunk 337 optimal weight: 4.9990 chunk 122 optimal weight: 0.0370 chunk 346 optimal weight: 0.0970 chunk 339 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 941 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.076174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047844 restraints weight = 157894.003| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.01 r_work: 0.2780 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44296 Z= 0.123 Angle : 0.654 16.868 61176 Z= 0.326 Chirality : 0.041 0.357 7120 Planarity : 0.003 0.049 6821 Dihedral : 21.536 176.311 8363 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.36 % Allowed : 28.51 % Favored : 70.13 % 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 aren not related in a simple way. whole: 0.75 (0.13), residues: 4723 helix: 1.57 (0.11), residues: 2282 sheet: 0.48 (0.20), residues: 688 loop : -0.92 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.023 0.001 TYR C 40 PHE 0.031 0.001 PHE H 73 TRP 0.074 0.002 TRP Q1396 HIS 0.005 0.001 HIS Q1316 Details of bonding type rmsd covalent geometry : bond 0.00282 (44294) covalent geometry : angle 0.65387 (61176) hydrogen bonds : bond 0.03414 ( 1956) hydrogen bonds : angle 3.51179 ( 5449) Misc. bond : bond 0.00095 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9446 Ramachandran restraints generated. 4723 Oldfield, 0 Emsley, 4723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8103 (mmtt) REVERT: A 59 GLU cc_start: 0.9252 (tp30) cc_final: 0.8986 (mp0) REVERT: A 64 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9212 (mppt) REVERT: A 105 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8974 (mm-30) REVERT: A 106 ASP cc_start: 0.8955 (m-30) cc_final: 0.8401 (p0) REVERT: C 37 ARG cc_start: 0.8687 (mpt180) cc_final: 0.8355 (mtm-85) REVERT: C 69 ASN cc_start: 0.9639 (m-40) cc_final: 0.9422 (p0) REVERT: C 114 GLN cc_start: 0.8815 (pm20) cc_final: 0.8525 (pm20) REVERT: D 88 LYS cc_start: 0.9499 (mmmm) cc_final: 0.9200 (mmpt) REVERT: E 76 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8311 (tp-100) REVERT: E 122 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8185 (tmtm) REVERT: G 58 TYR cc_start: 0.8856 (t80) cc_final: 0.8628 (t80) REVERT: G 90 ASN cc_start: 0.9345 (t0) cc_final: 0.9015 (t0) REVERT: H 46 LYS cc_start: 0.9309 (mtmm) cc_final: 0.9060 (mtmm) REVERT: H 96 GLU cc_start: 0.8968 (mp0) cc_final: 0.8385 (mp0) REVERT: H 116 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: Q 926 MET cc_start: 0.8489 (mmt) cc_final: 0.8191 (pmm) REVERT: Q 1316 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.6086 (t70) REVERT: Q 1324 MET cc_start: 0.7415 (mpp) cc_final: 0.6929 (mtt) REVERT: Q 1372 LEU cc_start: 0.8256 (mt) cc_final: 0.7707 (tp) REVERT: Q 1396 TRP cc_start: 0.5810 (t-100) cc_final: 0.5107 (t60) REVERT: T 269 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7093 (mpt) REVERT: U 86 MET cc_start: 0.9116 (mmm) cc_final: 0.8585 (tpp) REVERT: U 144 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8497 (tm-30) REVERT: W 212 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6500 (p90) REVERT: X 222 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7588 (t80) REVERT: Y 23 HIS cc_start: 0.9302 (OUTLIER) cc_final: 0.8760 (p90) REVERT: B 74 GLU cc_start: 0.9551 (tp30) cc_final: 0.9209 (pt0) REVERT: F 40 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7697 (mmp-170) REVERT: F 93 GLN cc_start: 0.9062 (mt0) cc_final: 0.8752 (tm-30) outliers start: 54 outliers final: 31 residues processed: 319 average time/residue: 0.6511 time to fit residues: 252.2106 Evaluate side-chains 304 residues out of total 4138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 450 ASP Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 378 optimal weight: 8.9990 chunk 306 optimal weight: 7.9990 chunk 362 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 82 optimal weight: 0.0070 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 456 optimal weight: 8.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 ASN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.076188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047846 restraints weight = 158631.403| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.02 r_work: 0.2773 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.194 44296 Z= 0.155 Angle : 0.728 59.191 61176 Z= 0.380 Chirality : 0.042 0.577 7120 Planarity : 0.003 0.049 6821 Dihedral : 21.535 176.317 8363 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.26 % Allowed : 28.64 % Favored : 70.10 % 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 aren not related in a simple way. whole: 0.74 (0.13), residues: 4723 helix: 1.55 (0.11), residues: 2282 sheet: 0.49 (0.20), residues: 688 loop : -0.92 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 72 TYR 0.031 0.001 TYR F 51 PHE 0.023 0.001 PHE H 73 TRP 0.059 0.002 TRP Q1396 HIS 0.005 0.001 HIS Q1316 Details of bonding type rmsd covalent geometry : bond 0.00342 (44294) covalent geometry : angle 0.72770 (61176) hydrogen bonds : bond 0.03427 ( 1956) hydrogen bonds : angle 3.51259 ( 5449) Misc. bond : bond 0.00094 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13350.60 seconds wall clock time: 227 minutes 46.40 seconds (13666.40 seconds total)