Starting phenix.real_space_refine on Sun Sep 13 12:11:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xhn_33196/09_2026/7xhn_33196.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xhn_33196/09_2026/7xhn_33196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xhn_33196/09_2026/7xhn_33196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xhn_33196/09_2026/7xhn_33196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xhn_33196/09_2026/7xhn_33196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xhn_33196/09_2026/7xhn_33196.map" } resolution = 3.71 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 187 atoms to isotropic. 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 50 5.49 5 S 116 5.16 5 C 14740 2.51 5 N 4033 2.21 5 O 4425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23364 Number of models: 1 Model: "" Number of chains: 20 Chain: "o" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 95 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1560 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 4111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4111 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 2, 'TRP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "K" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1869 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2422 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1298 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain: "N" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2493 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1588 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "P" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1808 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 790 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "T" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 804 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "W" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} 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: "c" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1175 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 699 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLU:plan': 14, 'ASN:plan1': 6, 'PHE:plan': 5, 'HIS:plan': 3, 'GLN:plan1': 11, 'ARG:plan': 8, 'TYR:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 250 Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 308 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 10, 'PHE:plan': 2, 'GLN:plan1': 4, 'ASN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 4.23, per 1000 atoms: 0.18 Number of scatterers: 23364 At special positions: 0 Unit cell: (106.14, 169.58, 187.88, 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 116 16.00 P 50 15.00 O 4425 8.00 N 4033 7.00 C 14740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 861.1 milliseconds 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 16 sheets defined 63.3% alpha, 5.7% beta 5 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'o' and resid 16 through 27 removed outlier: 3.746A pdb=" N ARG o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU o 25 " --> pdb=" O LEU o 21 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR o 26 " --> pdb=" O GLU o 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 66 removed outlier: 3.626A pdb=" N LEU H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 82 through 90 removed outlier: 5.094A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 117 removed outlier: 3.942A pdb=" N ILE H 98 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 removed outlier: 3.868A pdb=" N ASP H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 188 removed outlier: 3.888A pdb=" N GLU H 152 " --> pdb=" O TRP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 210 removed outlier: 4.337A pdb=" N ILE H 208 " --> pdb=" O MET H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 223 removed outlier: 3.795A pdb=" N GLY H 222 " --> pdb=" O ASN H 218 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 218 through 223' Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'I' and resid 63 through 76 Processing helix chain 'I' and resid 84 through 100 removed outlier: 3.644A pdb=" N LEU I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 138 through 146 removed outlier: 3.539A pdb=" N ASP I 142 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL I 145 " --> pdb=" O GLU I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 177 through 183 removed outlier: 3.938A pdb=" N ILE I 181 " --> pdb=" O ARG I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.765A pdb=" N PHE I 188 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 193 No H-bonds generated for 'chain 'I' and resid 191 through 193' Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.174A pdb=" N HIS I 203 " --> pdb=" O PRO I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 214 Processing helix chain 'I' and resid 215 through 229 Processing helix chain 'I' and resid 232 through 245 Processing helix chain 'I' and resid 268 through 282 removed outlier: 4.572A pdb=" N ALA I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 379 removed outlier: 3.817A pdb=" N HIS I 374 " --> pdb=" O SER I 370 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE I 376 " --> pdb=" O LEU I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 402 removed outlier: 3.916A pdb=" N TRP I 391 " --> pdb=" O ARG I 387 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS I 400 " --> pdb=" O LEU I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 405 No H-bonds generated for 'chain 'I' and resid 403 through 405' Processing helix chain 'I' and resid 409 through 429 removed outlier: 4.267A pdb=" N GLU I 413 " --> pdb=" O GLU I 409 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR I 415 " --> pdb=" O GLY I 411 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR I 420 " --> pdb=" O ASN I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.623A pdb=" N ALA I 437 " --> pdb=" O TYR I 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS I 441 " --> pdb=" O ALA I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.848A pdb=" N GLN I 457 " --> pdb=" O SER I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 514 removed outlier: 3.982A pdb=" N SER I 492 " --> pdb=" O TYR I 488 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP I 507 " --> pdb=" O ASN I 503 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP I 511 " --> pdb=" O TRP I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 551 removed outlier: 3.608A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR I 545 " --> pdb=" O GLY I 541 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR I 546 " --> pdb=" O TRP I 542 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET I 548 " --> pdb=" O SER I 544 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU I 551 " --> pdb=" O ALA I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 566 Processing helix chain 'I' and resid 571 through 576 Processing helix chain 'I' and resid 584 through 593 removed outlier: 4.400A pdb=" N SER I 590 " --> pdb=" O GLY I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 621 removed outlier: 4.279A pdb=" N GLN I 602 " --> pdb=" O SER I 598 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) Processing helix chain 'I' and resid 632 through 651 removed outlier: 3.675A pdb=" N MET I 647 " --> pdb=" O TYR I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 686 through 695 Processing helix chain 'I' and resid 716 through 726 Processing helix chain 'I' and resid 728 through 737 Processing helix chain 'K' and resid 21 through 46 removed outlier: 3.960A pdb=" N GLU K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 75 removed outlier: 4.174A pdb=" N SER K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 147 removed outlier: 3.559A pdb=" N GLU K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR K 110 " --> pdb=" O MET K 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 183 Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'K' and resid 208 through 223 removed outlier: 3.792A pdb=" N ARG K 222 " --> pdb=" O ILE K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 removed outlier: 3.531A pdb=" N VAL K 243 " --> pdb=" O TRP K 239 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU K 247 " --> pdb=" O VAL K 243 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 40 removed outlier: 3.621A pdb=" N PHE L 40 " --> pdb=" O LYS L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 69 removed outlier: 4.406A pdb=" N HIS L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 105 removed outlier: 3.525A pdb=" N PHE L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 172 removed outlier: 4.043A pdb=" N GLU L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 removed outlier: 4.470A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 226 removed outlier: 3.830A pdb=" N THR L 226 " --> pdb=" O ALA L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 269 removed outlier: 3.603A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.996A pdb=" N ARG L 293 " --> pdb=" O SER L 289 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 302 Processing helix chain 'L' and resid 327 through 344 Processing helix chain 'M' and resid 25 through 38 removed outlier: 4.209A pdb=" N GLU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 83 Processing helix chain 'M' and resid 84 through 88 removed outlier: 3.797A pdb=" N VAL M 88 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.589A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 140 Processing helix chain 'M' and resid 142 through 154 removed outlier: 3.748A pdb=" N ARG M 148 " --> pdb=" O GLN M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 167 removed outlier: 3.623A pdb=" N LEU M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 20 through 28 removed outlier: 3.663A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA N 27 " --> pdb=" O THR N 23 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 39 removed outlier: 4.025A pdb=" N GLN N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR N 38 " --> pdb=" O ASN N 34 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL N 39 " --> pdb=" O GLN N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 58 removed outlier: 4.084A pdb=" N ILE N 53 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 removed outlier: 3.796A pdb=" N LEU N 68 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 4.019A pdb=" N ILE N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA N 115 " --> pdb=" O ILE N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 removed outlier: 3.836A pdb=" N ALA N 203 " --> pdb=" O ASP N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 252 removed outlier: 3.685A pdb=" N ARG N 247 " --> pdb=" O VAL N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 308 Processing helix chain 'N' and resid 320 through 325 removed outlier: 3.556A pdb=" N THR N 324 " --> pdb=" O SER N 320 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 100 Processing helix chain 'O' and resid 100 through 109 removed outlier: 4.150A pdb=" N ILE O 104 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 168 Processing helix chain 'O' and resid 176 through 184 removed outlier: 3.509A pdb=" N GLU O 182 " --> pdb=" O PHE O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 192 Processing helix chain 'O' and resid 192 through 200 removed outlier: 3.518A pdb=" N SER O 199 " --> pdb=" O ASP O 195 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP O 200 " --> pdb=" O ARG O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 215 Processing helix chain 'O' and resid 261 through 278 removed outlier: 3.520A pdb=" N THR O 277 " --> pdb=" O THR O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 291 Processing helix chain 'O' and resid 292 through 295 removed outlier: 3.847A pdb=" N ASP O 295 " --> pdb=" O GLU O 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 292 through 295' Processing helix chain 'P' and resid 63 through 73 Processing helix chain 'P' and resid 90 through 94 removed outlier: 4.140A pdb=" N MET P 93 " --> pdb=" O SER P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 148 Processing helix chain 'P' and resid 152 through 157 Processing helix chain 'P' and resid 165 through 191 removed outlier: 3.923A pdb=" N HIS P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU P 175 " --> pdb=" O HIS P 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR P 183 " --> pdb=" O TYR P 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU P 189 " --> pdb=" O LYS P 185 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 269 removed outlier: 4.198A pdb=" N ARG P 263 " --> pdb=" O PRO P 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR P 264 " --> pdb=" O LEU P 260 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY P 267 " --> pdb=" O ARG P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 283 removed outlier: 3.625A pdb=" N LEU P 275 " --> pdb=" O ILE P 271 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 35 Processing helix chain 'S' and resid 43 through 72 removed outlier: 3.756A pdb=" N MET S 67 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 86 removed outlier: 3.588A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 106 removed outlier: 3.641A pdb=" N ASP S 98 " --> pdb=" O LYS S 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 472 Processing helix chain 'T' and resid 476 through 505 removed outlier: 3.707A pdb=" N MET T 482 " --> pdb=" O LYS T 478 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASP T 496 " --> pdb=" O GLN T 492 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.546A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU T 518 " --> pdb=" O ASP T 514 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.649A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG T 537 " --> pdb=" O VAL T 533 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS T 538 " --> pdb=" O LEU T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 removed outlier: 4.377A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU T 547 " --> pdb=" O TYR T 543 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 removed outlier: 3.750A pdb=" N LEU W 22 " --> pdb=" O PRO W 18 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS W 23 " --> pdb=" O ARG W 19 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS W 30 " --> pdb=" O PHE W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 66 Processing helix chain 'W' and resid 71 through 86 removed outlier: 4.019A pdb=" N ALA W 77 " --> pdb=" O GLU W 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 80 " --> pdb=" O LEU W 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.591A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS X 22 " --> pdb=" O LEU X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 61 removed outlier: 3.768A pdb=" N LEU X 37 " --> pdb=" O ASP X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 81 removed outlier: 3.911A pdb=" N LEU X 70 " --> pdb=" O ASP X 66 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 4.154A pdb=" N LEU X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 100 Processing helix chain 'Q' and resid 102 through 121 Processing helix chain 'Q' and resid 131 through 195 Processing helix chain 'Q' and resid 226 through 231 removed outlier: 3.907A pdb=" N ALA Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 226 through 231' Processing helix chain 'Q' and resid 236 through 268 removed outlier: 3.538A pdb=" N GLN Q 250 " --> pdb=" O HIS Q 246 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE Q 257 " --> pdb=" O SER Q 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 268 Proline residue: U 256 - end of helix Processing helix chain 'U' and resid 271 through 366 removed outlier: 4.055A pdb=" N ILE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Proline residue: U 332 - end of helix removed outlier: 3.838A pdb=" N LEU U 351 " --> pdb=" O ARG U 347 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG U 352 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR U 356 " --> pdb=" O ARG U 352 " (cutoff:3.500A) Processing helix chain 'U' and resid 385 through 403 removed outlier: 3.786A pdb=" N LEU U 398 " --> pdb=" O ALA U 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 107 removed outlier: 3.665A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 113 Processing helix chain 'R' and resid 132 through 150 removed outlier: 4.417A pdb=" N MET R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS R 145 " --> pdb=" O GLU R 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 253 through 254 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'L' and resid 118 through 123 removed outlier: 3.611A pdb=" N GLN L 140 " --> pdb=" O ILE L 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 251 through 253 removed outlier: 5.956A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 17 through 21 removed outlier: 6.716A pdb=" N THR M 17 " --> pdb=" O ILE M 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AA7, first strand: chain 'N' and resid 160 through 164 removed outlier: 6.342A pdb=" N TRP N 83 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU N 193 " --> pdb=" O TRP N 83 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL N 85 " --> pdb=" O MET N 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 120 through 122 removed outlier: 3.545A pdb=" N ALA N 136 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N VAL N 131 " --> pdb=" O TYR N 151 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N TYR N 151 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N ILE N 133 " --> pdb=" O PRO N 149 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N ILE N 135 " --> pdb=" O TYR N 147 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TYR N 147 " --> pdb=" O ILE N 135 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP N 137 " --> pdb=" O ASN N 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 267 through 269 removed outlier: 3.727A pdb=" N PHE N 297 " --> pdb=" O ALA N 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 272 through 273 removed outlier: 3.992A pdb=" N THR N 273 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 114 through 116 removed outlier: 3.712A pdb=" N SER O 114 " --> pdb=" O CYS O 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 217 through 221 removed outlier: 3.747A pdb=" N THR O 253 " --> pdb=" O CYS O 234 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 78 through 86 removed outlier: 5.451A pdb=" N ILE P 78 " --> pdb=" O ASN P 110 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN P 110 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU P 123 " --> pdb=" O VAL P 135 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL P 135 " --> pdb=" O LEU P 123 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE P 125 " --> pdb=" O SER P 133 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER P 133 " --> pdb=" O ILE P 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 196 through 197 Processing sheet with id=AB6, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AB7, first strand: chain 'T' and resid 509 through 510 removed outlier: 3.550A pdb=" N VAL T 510 " --> pdb=" O ARG W 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 1308 hydrogen bonds defined for protein. 3837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.32: 3851 1.32 - 1.60: 19744 1.60 - 1.88: 267 1.88 - 2.16: 0 2.16 - 2.44: 1 Bond restraints: 23863 Sorted by residual: bond pdb=" CB PRO O 208 " pdb=" CG PRO O 208 " ideal model delta sigma weight residual 1.492 2.440 -0.948 5.00e-02 4.00e+02 3.60e+02 bond pdb=" CA PRO K 259 " pdb=" CB PRO K 259 " ideal model delta sigma weight residual 1.531 1.623 -0.091 6.20e-03 2.60e+04 2.17e+02 bond pdb=" CG PRO O 208 " pdb=" CD PRO O 208 " ideal model delta sigma weight residual 1.503 1.035 0.468 3.40e-02 8.65e+02 1.90e+02 bond pdb=" CG LEU M 52 " pdb=" CD2 LEU M 52 " ideal model delta sigma weight residual 1.521 1.079 0.442 3.30e-02 9.18e+02 1.80e+02 bond pdb=" N PRO O 208 " pdb=" CA PRO O 208 " ideal model delta sigma weight residual 1.465 1.363 0.101 1.15e-02 7.56e+03 7.78e+01 ... (remaining 23858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 32473 21.21 - 42.42: 4 42.42 - 63.63: 0 63.63 - 84.84: 0 84.84 - 106.05: 1 Bond angle restraints: 32478 Sorted by residual: angle pdb=" CB PRO O 208 " pdb=" CG PRO O 208 " pdb=" CD PRO O 208 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO O 208 " pdb=" N PRO O 208 " pdb=" CD PRO O 208 " ideal model delta sigma weight residual 112.00 82.02 29.98 1.40e+00 5.10e-01 4.59e+02 angle pdb=" CA PRO M 53 " pdb=" N PRO M 53 " pdb=" CD PRO M 53 " ideal model delta sigma weight residual 112.00 94.02 17.98 1.40e+00 5.10e-01 1.65e+02 angle pdb=" CA PRO O 208 " pdb=" CB PRO O 208 " pdb=" CG PRO O 208 " ideal model delta sigma weight residual 104.50 80.52 23.98 1.90e+00 2.77e-01 1.59e+02 angle pdb=" N PRO O 208 " pdb=" CD PRO O 208 " pdb=" CG PRO O 208 " ideal model delta sigma weight residual 103.20 84.53 18.67 1.50e+00 4.44e-01 1.55e+02 ... (remaining 32473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 12561 22.71 - 45.42: 1471 45.42 - 68.14: 291 68.14 - 90.85: 41 90.85 - 113.56: 1 Dihedral angle restraints: 14365 sinusoidal: 5835 harmonic: 8530 Sorted by residual: dihedral pdb=" CD ARG P 168 " pdb=" NE ARG P 168 " pdb=" CZ ARG P 168 " pdb=" NH1 ARG P 168 " ideal model delta sinusoidal sigma weight residual 0.00 68.03 -68.03 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CD ARG H 47 " pdb=" NE ARG H 47 " pdb=" CZ ARG H 47 " pdb=" NH1 ARG H 47 " ideal model delta sinusoidal sigma weight residual 0.00 -63.46 63.46 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CA TYR T 552 " pdb=" C TYR T 552 " pdb=" N SER T 553 " pdb=" CA SER T 553 " ideal model delta harmonic sigma weight residual -180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 14362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 3752 0.174 - 0.347: 42 0.347 - 0.521: 1 0.521 - 0.694: 3 0.694 - 0.868: 1 Chirality restraints: 3799 Sorted by residual: chirality pdb=" CG LEU M 52 " pdb=" CB LEU M 52 " pdb=" CD1 LEU M 52 " pdb=" CD2 LEU M 52 " both_signs ideal model delta sigma weight residual False -2.59 -1.72 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CG LEU I 558 " pdb=" CB LEU I 558 " pdb=" CD1 LEU I 558 " pdb=" CD2 LEU I 558 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CG LEU K 67 " pdb=" CB LEU K 67 " pdb=" CD1 LEU K 67 " pdb=" CD2 LEU K 67 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 3796 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 168 " -1.022 9.50e-02 1.11e+02 4.58e-01 1.27e+02 pdb=" NE ARG P 168 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG P 168 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG P 168 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG P 168 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 47 " 0.982 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG H 47 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG H 47 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 47 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 47 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 724 " 0.028 2.00e-02 2.50e+03 5.26e-02 4.85e+01 pdb=" CG PHE I 724 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE I 724 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE I 724 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE I 724 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE I 724 " -0.078 2.00e-02 2.50e+03 pdb=" CZ PHE I 724 " 0.088 2.00e-02 2.50e+03 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 176 2.44 - 3.06: 16042 3.06 - 3.67: 39766 3.67 - 4.29: 56432 4.29 - 4.90: 87990 Nonbonded interactions: 200406 Sorted by model distance: nonbonded pdb=" OE1 GLN O 210 " pdb=" OG SER O 219 " model vdw 1.828 3.040 nonbonded pdb=" O ASN Q 181 " pdb=" NE2 GLN Q 184 " model vdw 1.912 3.120 nonbonded pdb=" CE MET P 165 " pdb=" CD ARG P 168 " model vdw 1.925 3.860 nonbonded pdb=" NH1 ARG Q 145 " pdb=" CB LYS U 308 " model vdw 1.928 3.520 nonbonded pdb=" OD2 ASP O 141 " pdb=" ND1 HIS O 151 " model vdw 2.017 3.120 ... (remaining 200401 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.830 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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 : 0.011 0.948 23863 Z= 0.459 Angle : 1.266 106.053 32478 Z= 0.676 Chirality : 0.059 0.868 3799 Planarity : 0.012 0.458 3940 Dihedral : 19.322 113.560 8757 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 35.16 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.60 % Favored : 90.72 % Rotamer: Outliers : 1.25 % Allowed : 29.41 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.15), residues: 2814 helix: -1.24 (0.12), residues: 1632 sheet: -3.77 (0.31), residues: 195 loop : -2.54 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG X 17 TYR 0.105 0.003 TYR T 470 PHE 0.088 0.003 PHE I 724 TRP 0.105 0.004 TRP P 176 HIS 0.031 0.002 HIS Q 109 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.46 (23863) covalent geometry : angle 1.26646 / 0.68 (32478) hydrogen bonds : bond 0.21666 / 14.01 ( 1320) hydrogen bonds : angle 9.39852 / 6.49 ( 3861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 434 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 112 LEU cc_start: 0.8281 (tt) cc_final: 0.8068 (tp) outliers start: 29 outliers final: 18 residues processed: 445 average time/residue: 0.1615 time to fit residues: 110.7953 Evaluate side-chains 433 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 415 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain K residue 239 TRP Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 201 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 142 MET Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain T residue 536 GLU Chi-restraints excluded: chain X residue 38 MET Chi-restraints excluded: chain Q residue 83 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 144 GLN I 123 ASN I 182 ASN I 213 ASN I 397 GLN I 480 GLN I 641 ASN I 642 HIS I 726 GLN I 729 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN L 71 GLN L 290 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN N 106 ASN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 HIS N 208 GLN N 239 HIS ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN O 210 GLN ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 532 HIS T 538 HIS X 56 GLN Q 184 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.160033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.128205 restraints weight = 54555.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.125613 restraints weight = 53365.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.127093 restraints weight = 43884.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.129473 restraints weight = 33060.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.129167 restraints weight = 26884.259| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 23863 Z= 0.221 Angle : 0.866 15.435 32478 Z= 0.442 Chirality : 0.048 0.294 3799 Planarity : 0.006 0.070 3940 Dihedral : 15.073 87.486 3609 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.67 % Favored : 90.90 % Rotamer: Outliers : 4.87 % Allowed : 24.38 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.15), residues: 2814 helix: -1.09 (0.12), residues: 1704 sheet: -3.85 (0.30), residues: 186 loop : -2.85 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 17 TYR 0.023 0.002 TYR N 155 PHE 0.040 0.002 PHE I 734 TRP 0.037 0.003 TRP H 148 HIS 0.018 0.002 HIS Q 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (23863) covalent geometry : angle 0.86551 / 0.44 (32478) hydrogen bonds : bond 0.06274 / 4.03 ( 1320) hydrogen bonds : angle 6.94062 / 4.78 ( 3861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 470 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.6637 (ptm160) cc_final: 0.6344 (ptm-80) REVERT: H 106 MET cc_start: 0.7798 (mmm) cc_final: 0.7463 (mmm) REVERT: H 154 LEU cc_start: 0.8836 (mt) cc_final: 0.8624 (mt) REVERT: H 189 MET cc_start: 0.6209 (mpp) cc_final: 0.5244 (mpp) REVERT: I 132 CYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6829 (p) REVERT: I 214 VAL cc_start: 0.9237 (t) cc_final: 0.8994 (t) REVERT: I 440 TYR cc_start: 0.8169 (m-80) cc_final: 0.7964 (m-80) REVERT: I 474 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8233 (tt) REVERT: I 570 ASP cc_start: 0.6977 (p0) cc_final: 0.6556 (p0) REVERT: I 691 TYR cc_start: 0.6677 (m-80) cc_final: 0.6351 (m-80) REVERT: I 726 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6883 (mm-40) REVERT: K 26 ARG cc_start: 0.7795 (tmm160) cc_final: 0.7381 (tmm160) REVERT: K 27 GLU cc_start: 0.7776 (pm20) cc_final: 0.7439 (pm20) REVERT: L 31 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5842 (mm) REVERT: L 205 ASP cc_start: 0.8135 (t0) cc_final: 0.7886 (t0) REVERT: N 169 ARG cc_start: 0.6669 (mtm180) cc_final: 0.6312 (mtm180) REVERT: N 171 ASN cc_start: 0.7423 (p0) cc_final: 0.7181 (p0) REVERT: N 191 MET cc_start: 0.8362 (tpp) cc_final: 0.7939 (ttt) REVERT: P 136 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.7039 (p) REVERT: S 19 LEU cc_start: 0.8654 (mt) cc_final: 0.8153 (mt) REVERT: X 74 LEU cc_start: 0.9026 (mm) cc_final: 0.8735 (pp) outliers start: 113 outliers final: 51 residues processed: 543 average time/residue: 0.1662 time to fit residues: 139.1027 Evaluate side-chains 468 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 412 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 726 GLN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 141 ASP Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 174 GLN Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain T residue 466 LEU Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain Q residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 41 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 230 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 554 ASN I 726 GLN K 54 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS Q 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.160096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.126952 restraints weight = 54406.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.125113 restraints weight = 43989.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125776 restraints weight = 35544.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.126250 restraints weight = 31647.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.126408 restraints weight = 29433.067| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23863 Z= 0.189 Angle : 0.824 19.470 32478 Z= 0.418 Chirality : 0.046 0.257 3799 Planarity : 0.005 0.073 3940 Dihedral : 14.782 86.428 3582 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.39 % Favored : 91.19 % Rotamer: Outliers : 4.87 % Allowed : 24.59 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.15), residues: 2814 helix: -0.87 (0.12), residues: 1730 sheet: -3.37 (0.34), residues: 171 loop : -2.85 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 52 TYR 0.040 0.002 TYR T 470 PHE 0.044 0.002 PHE K 97 TRP 0.033 0.002 TRP H 148 HIS 0.011 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (23863) covalent geometry : angle 0.82394 / 0.42 (32478) hydrogen bonds : bond 0.05733 / 3.67 ( 1320) hydrogen bonds : angle 6.56681 / 4.53 ( 3861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 450 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.6318 (ptm160) cc_final: 0.6086 (ptm-80) REVERT: H 154 LEU cc_start: 0.8903 (mt) cc_final: 0.8694 (mt) REVERT: H 189 MET cc_start: 0.6213 (mpp) cc_final: 0.5718 (mmp) REVERT: I 73 PHE cc_start: 0.3908 (m-80) cc_final: 0.3313 (m-10) REVERT: I 132 CYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6566 (p) REVERT: I 214 VAL cc_start: 0.9192 (t) cc_final: 0.8945 (t) REVERT: I 428 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8786 (tt) REVERT: I 456 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8612 (mp) REVERT: I 491 CYS cc_start: 0.7918 (m) cc_final: 0.7678 (m) REVERT: I 570 ASP cc_start: 0.6951 (p0) cc_final: 0.6606 (p0) REVERT: I 726 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6945 (tp-100) REVERT: L 31 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.4687 (mm) REVERT: L 205 ASP cc_start: 0.8139 (t0) cc_final: 0.7778 (t0) REVERT: L 319 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6843 (pptt) REVERT: M 76 TYR cc_start: 0.8610 (t80) cc_final: 0.7968 (t80) REVERT: M 79 GLN cc_start: 0.7666 (mp10) cc_final: 0.7396 (mp10) REVERT: M 93 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8101 (t80) REVERT: N 171 ASN cc_start: 0.7210 (p0) cc_final: 0.6984 (p0) REVERT: N 191 MET cc_start: 0.8306 (tpp) cc_final: 0.7998 (ttm) REVERT: O 174 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5975 (tm-30) REVERT: O 212 ASN cc_start: 0.7706 (m-40) cc_final: 0.7346 (m-40) REVERT: O 296 MET cc_start: 0.6655 (mmm) cc_final: 0.5502 (mmm) REVERT: P 136 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.6995 (p) REVERT: T 485 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8079 (pttp) REVERT: T 519 MET cc_start: 0.8230 (mtt) cc_final: 0.7888 (mtm) REVERT: W 52 HIS cc_start: 0.8019 (t70) cc_final: 0.7315 (t70) REVERT: X 38 MET cc_start: 0.6309 (tmm) cc_final: 0.5927 (tmm) outliers start: 113 outliers final: 53 residues processed: 528 average time/residue: 0.1534 time to fit residues: 126.0575 Evaluate side-chains 471 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 408 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 726 GLN Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 174 GLN Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 466 LEU Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain Q residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 158 optimal weight: 0.5980 chunk 244 optimal weight: 50.0000 chunk 201 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 729 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 210 GLN ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS Q 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.160058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.127467 restraints weight = 54313.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125362 restraints weight = 47531.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.126470 restraints weight = 40072.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.127519 restraints weight = 32101.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.127432 restraints weight = 28774.373| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23863 Z= 0.198 Angle : 0.816 15.798 32478 Z= 0.412 Chirality : 0.046 0.222 3799 Planarity : 0.005 0.087 3940 Dihedral : 14.746 87.042 3580 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.39 % Favored : 91.19 % Rotamer: Outliers : 5.56 % Allowed : 25.06 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 2814 helix: -0.72 (0.12), residues: 1735 sheet: -3.21 (0.35), residues: 171 loop : -2.82 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 147 TYR 0.020 0.002 TYR I 440 PHE 0.027 0.002 PHE K 188 TRP 0.033 0.002 TRP N 28 HIS 0.011 0.001 HIS P 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (23863) covalent geometry : angle 0.81645 / 0.41 (32478) hydrogen bonds : bond 0.05428 / 3.48 ( 1320) hydrogen bonds : angle 6.37598 / 4.39 ( 3861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 438 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.6461 (ptm160) cc_final: 0.6223 (ptm-80) REVERT: H 106 MET cc_start: 0.7790 (mmm) cc_final: 0.7470 (mmm) REVERT: H 154 LEU cc_start: 0.8899 (mt) cc_final: 0.8693 (mt) REVERT: H 189 MET cc_start: 0.6476 (mpp) cc_final: 0.6104 (mmt) REVERT: I 132 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6351 (p) REVERT: I 214 VAL cc_start: 0.9151 (t) cc_final: 0.8899 (t) REVERT: I 428 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8734 (tt) REVERT: I 491 CYS cc_start: 0.7820 (m) cc_final: 0.7608 (m) REVERT: I 570 ASP cc_start: 0.6882 (p0) cc_final: 0.6592 (p0) REVERT: I 604 CYS cc_start: 0.6337 (OUTLIER) cc_final: 0.5999 (t) REVERT: I 643 TYR cc_start: 0.7755 (m-10) cc_final: 0.7381 (m-10) REVERT: I 647 MET cc_start: 0.7640 (ppp) cc_final: 0.7320 (ppp) REVERT: K 223 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6764 (pp) REVERT: L 205 ASP cc_start: 0.8169 (t0) cc_final: 0.7769 (t0) REVERT: L 319 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6771 (pptt) REVERT: M 76 TYR cc_start: 0.8626 (t80) cc_final: 0.8012 (t80) REVERT: M 79 GLN cc_start: 0.7765 (mt0) cc_final: 0.7534 (mp10) REVERT: M 170 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7327 (ttm110) REVERT: N 69 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8236 (tt) REVERT: N 191 MET cc_start: 0.8254 (tpp) cc_final: 0.7948 (ttm) REVERT: N 295 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8421 (mm) REVERT: O 296 MET cc_start: 0.6458 (mmm) cc_final: 0.5232 (mmm) REVERT: P 136 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6989 (p) REVERT: S 40 MET cc_start: 0.4958 (tpp) cc_final: 0.4670 (tpp) REVERT: S 53 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7548 (mm) REVERT: T 485 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8007 (pttp) REVERT: X 20 HIS cc_start: 0.7644 (m90) cc_final: 0.7247 (m-70) REVERT: X 38 MET cc_start: 0.6375 (tmm) cc_final: 0.6148 (tmm) REVERT: Q 196 ARG cc_start: 0.4834 (OUTLIER) cc_final: 0.3732 (mmp80) outliers start: 129 outliers final: 71 residues processed: 529 average time/residue: 0.1581 time to fit residues: 129.9552 Evaluate side-chains 488 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 406 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 466 LEU Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 495 CYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 196 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 262 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 171 optimal weight: 0.2980 chunk 284 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 132 HIS I 726 GLN K 54 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS Q 184 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.159300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.125535 restraints weight = 53796.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.122927 restraints weight = 47717.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.123858 restraints weight = 38897.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.124268 restraints weight = 33276.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.124745 restraints weight = 32511.524| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23863 Z= 0.216 Angle : 0.835 15.742 32478 Z= 0.419 Chirality : 0.046 0.362 3799 Planarity : 0.005 0.073 3940 Dihedral : 14.728 87.028 3580 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.56 % Favored : 91.04 % Rotamer: Outliers : 5.73 % Allowed : 26.18 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.15), residues: 2814 helix: -0.59 (0.12), residues: 1732 sheet: -3.19 (0.34), residues: 171 loop : -2.84 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 147 TYR 0.035 0.002 TYR P 179 PHE 0.022 0.002 PHE O 110 TRP 0.033 0.002 TRP N 28 HIS 0.010 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (23863) covalent geometry : angle 0.83516 / 0.42 (32478) hydrogen bonds : bond 0.05297 / 3.40 ( 1320) hydrogen bonds : angle 6.25459 / 4.31 ( 3861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 421 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.6891 (ptm160) cc_final: 0.6597 (ptm-80) REVERT: H 137 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8132 (t0) REVERT: H 189 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.6259 (mmt) REVERT: I 132 CYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6643 (p) REVERT: I 171 MET cc_start: 0.5882 (tmm) cc_final: 0.5535 (tmm) REVERT: I 214 VAL cc_start: 0.9224 (t) cc_final: 0.8958 (t) REVERT: I 229 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5997 (mmm) REVERT: I 428 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8783 (tt) REVERT: I 643 TYR cc_start: 0.7752 (m-10) cc_final: 0.7475 (m-10) REVERT: I 647 MET cc_start: 0.7682 (ppp) cc_final: 0.7382 (ppp) REVERT: I 726 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7070 (mt0) REVERT: K 67 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7698 (mm) REVERT: K 80 GLU cc_start: 0.6020 (tp30) cc_final: 0.5740 (tp30) REVERT: K 223 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6890 (pp) REVERT: L 205 ASP cc_start: 0.8210 (t0) cc_final: 0.7822 (t0) REVERT: L 319 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6968 (pptt) REVERT: M 170 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7318 (ttm110) REVERT: N 69 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8552 (tt) REVERT: N 191 MET cc_start: 0.8331 (tpp) cc_final: 0.7951 (ttm) REVERT: N 295 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8406 (mm) REVERT: O 296 MET cc_start: 0.6576 (mmm) cc_final: 0.5357 (mmm) REVERT: P 136 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.7090 (p) REVERT: S 95 TYR cc_start: 0.7402 (t80) cc_final: 0.7191 (t80) REVERT: W 52 HIS cc_start: 0.8195 (t70) cc_final: 0.7972 (t70) REVERT: X 20 HIS cc_start: 0.7742 (m90) cc_final: 0.7385 (m-70) REVERT: X 45 PHE cc_start: 0.8214 (t80) cc_final: 0.7821 (t80) REVERT: Q 93 MET cc_start: 0.8142 (mtm) cc_final: 0.7751 (mmm) REVERT: Q 196 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.3765 (mmp80) outliers start: 133 outliers final: 80 residues processed: 510 average time/residue: 0.1620 time to fit residues: 128.1163 Evaluate side-chains 491 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 398 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 174 PHE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 502 GLN Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 695 PHE Chi-restraints excluded: chain I residue 726 GLN Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 495 CYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 189 GLU Chi-restraints excluded: chain Q residue 196 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 204 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS I 726 GLN K 54 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN L 140 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.159118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.126162 restraints weight = 54375.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.124103 restraints weight = 51361.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.125070 restraints weight = 41942.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125592 restraints weight = 34333.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.125718 restraints weight = 32854.125| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23863 Z= 0.211 Angle : 0.835 15.370 32478 Z= 0.418 Chirality : 0.047 0.334 3799 Planarity : 0.005 0.085 3940 Dihedral : 14.675 87.164 3576 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.56 % Favored : 91.04 % Rotamer: Outliers : 5.90 % Allowed : 26.66 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.15), residues: 2814 helix: -0.49 (0.12), residues: 1738 sheet: -3.18 (0.37), residues: 145 loop : -2.88 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 147 TYR 0.017 0.002 TYR L 207 PHE 0.047 0.002 PHE Q 112 TRP 0.037 0.002 TRP N 28 HIS 0.010 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (23863) covalent geometry : angle 0.83515 / 0.42 (32478) hydrogen bonds : bond 0.05127 / 3.30 ( 1320) hydrogen bonds : angle 6.15595 / 4.23 ( 3861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 424 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.7018 (ptm160) cc_final: 0.6715 (ptm-80) REVERT: H 47 ARG cc_start: 0.8303 (tmm-80) cc_final: 0.8053 (tmm-80) REVERT: H 106 MET cc_start: 0.7834 (mmm) cc_final: 0.7558 (mmm) REVERT: I 132 CYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6823 (p) REVERT: I 167 TRP cc_start: 0.6337 (t60) cc_final: 0.6119 (t60) REVERT: I 214 VAL cc_start: 0.9251 (t) cc_final: 0.8989 (t) REVERT: I 229 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5992 (mmm) REVERT: I 428 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8792 (tt) REVERT: I 604 CYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6235 (t) REVERT: I 642 HIS cc_start: 0.6843 (t-170) cc_final: 0.6480 (t-170) REVERT: I 643 TYR cc_start: 0.7800 (m-10) cc_final: 0.7448 (m-10) REVERT: I 647 MET cc_start: 0.7731 (ppp) cc_final: 0.7441 (ppp) REVERT: K 80 GLU cc_start: 0.6017 (tp30) cc_final: 0.5737 (tp30) REVERT: K 223 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6906 (pp) REVERT: L 70 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8480 (mtpp) REVERT: L 205 ASP cc_start: 0.8310 (t0) cc_final: 0.7901 (t0) REVERT: L 319 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6738 (pptt) REVERT: M 79 GLN cc_start: 0.7846 (mp10) cc_final: 0.7634 (mp10) REVERT: M 170 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7328 (ttm110) REVERT: N 69 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8391 (tt) REVERT: N 191 MET cc_start: 0.8389 (tpp) cc_final: 0.8032 (ttm) REVERT: N 295 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (mm) REVERT: O 296 MET cc_start: 0.6512 (mmm) cc_final: 0.5411 (mmm) REVERT: P 113 MET cc_start: 0.4923 (mpp) cc_final: 0.2816 (mmt) REVERT: S 94 LYS cc_start: 0.8495 (pptt) cc_final: 0.8005 (tppt) REVERT: T 485 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8459 (pptt) REVERT: T 536 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7292 (mm-30) REVERT: X 20 HIS cc_start: 0.7629 (m90) cc_final: 0.7265 (m-70) REVERT: X 43 LYS cc_start: 0.7828 (tttp) cc_final: 0.7531 (mttt) REVERT: X 45 PHE cc_start: 0.8203 (t80) cc_final: 0.7948 (t80) REVERT: Q 93 MET cc_start: 0.8124 (mtm) cc_final: 0.7704 (mmm) REVERT: Q 196 ARG cc_start: 0.4559 (OUTLIER) cc_final: 0.3868 (mmp80) outliers start: 137 outliers final: 84 residues processed: 517 average time/residue: 0.1597 time to fit residues: 127.6580 Evaluate side-chains 486 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 392 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 559 HIS Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 695 PHE Chi-restraints excluded: chain I residue 726 GLN Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain P residue 283 CYS Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 495 CYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 189 GLU Chi-restraints excluded: chain Q residue 196 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 126 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 274 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN I 602 GLN I 726 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.159796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.126490 restraints weight = 54198.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.124833 restraints weight = 45494.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.125687 restraints weight = 42346.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.126052 restraints weight = 37064.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.126372 restraints weight = 30742.313| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 23863 Z= 0.180 Angle : 0.835 14.879 32478 Z= 0.416 Chirality : 0.047 0.323 3799 Planarity : 0.005 0.059 3940 Dihedral : 14.615 87.479 3576 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.21 % Favored : 91.40 % Rotamer: Outliers : 4.91 % Allowed : 28.38 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.15), residues: 2814 helix: -0.43 (0.12), residues: 1744 sheet: -3.08 (0.35), residues: 159 loop : -2.86 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 248 TYR 0.044 0.002 TYR S 95 PHE 0.058 0.002 PHE K 97 TRP 0.041 0.002 TRP N 28 HIS 0.008 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (23863) covalent geometry : angle 0.83464 / 0.42 (32478) hydrogen bonds : bond 0.04956 / 3.19 ( 1320) hydrogen bonds : angle 6.04735 / 4.16 ( 3861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 429 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.6914 (ptm160) cc_final: 0.6651 (ptm-80) REVERT: H 47 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7914 (tmm-80) REVERT: H 65 GLU cc_start: 0.8400 (tt0) cc_final: 0.7797 (tm-30) REVERT: H 106 MET cc_start: 0.7865 (mmm) cc_final: 0.7587 (mmm) REVERT: H 162 LEU cc_start: 0.8998 (tp) cc_final: 0.8791 (tp) REVERT: I 111 ILE cc_start: 0.7310 (mm) cc_final: 0.7110 (mm) REVERT: I 132 CYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6238 (p) REVERT: I 214 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8876 (t) REVERT: I 229 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5836 (mmm) REVERT: I 428 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8672 (tt) REVERT: I 604 CYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6131 (t) REVERT: I 642 HIS cc_start: 0.6739 (t-170) cc_final: 0.6414 (t-170) REVERT: I 643 TYR cc_start: 0.7733 (m-10) cc_final: 0.7412 (m-10) REVERT: K 80 GLU cc_start: 0.5908 (tp30) cc_final: 0.5673 (tp30) REVERT: K 223 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6867 (pp) REVERT: L 30 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.6903 (tpp80) REVERT: L 205 ASP cc_start: 0.8044 (t0) cc_final: 0.7842 (t0) REVERT: L 319 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6614 (pptt) REVERT: N 69 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8319 (tt) REVERT: N 191 MET cc_start: 0.8282 (tpp) cc_final: 0.7970 (ttm) REVERT: O 296 MET cc_start: 0.6428 (mmm) cc_final: 0.5396 (mmm) REVERT: P 113 MET cc_start: 0.4870 (mpp) cc_final: 0.2871 (mmt) REVERT: P 179 TYR cc_start: 0.7899 (m-80) cc_final: 0.7688 (m-80) REVERT: S 40 MET cc_start: 0.4920 (tpp) cc_final: 0.4590 (tpp) REVERT: S 52 GLU cc_start: 0.7973 (pp20) cc_final: 0.7572 (pp20) REVERT: S 94 LYS cc_start: 0.8611 (pptt) cc_final: 0.8042 (tppt) REVERT: T 485 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8487 (pptt) REVERT: X 20 HIS cc_start: 0.7648 (m90) cc_final: 0.7279 (m-70) REVERT: Q 93 MET cc_start: 0.8072 (mtm) cc_final: 0.7572 (mmm) REVERT: Q 196 ARG cc_start: 0.4381 (OUTLIER) cc_final: 0.3861 (mmp80) outliers start: 114 outliers final: 80 residues processed: 504 average time/residue: 0.1650 time to fit residues: 128.5433 Evaluate side-chains 501 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 410 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 451 CYS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain P residue 283 CYS Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 533 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Q residue 83 HIS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 184 GLN Chi-restraints excluded: chain Q residue 189 GLU Chi-restraints excluded: chain Q residue 196 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 255 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 140 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.160123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.127381 restraints weight = 54254.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.125726 restraints weight = 43786.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126842 restraints weight = 38024.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.127305 restraints weight = 32261.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.127424 restraints weight = 28438.603| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23863 Z= 0.174 Angle : 0.840 14.111 32478 Z= 0.421 Chirality : 0.046 0.240 3799 Planarity : 0.005 0.059 3940 Dihedral : 14.512 87.567 3576 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.07 % Favored : 91.58 % Rotamer: Outliers : 5.17 % Allowed : 28.25 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.15), residues: 2814 helix: -0.35 (0.12), residues: 1748 sheet: -2.94 (0.36), residues: 159 loop : -2.82 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 380 TYR 0.038 0.002 TYR P 179 PHE 0.042 0.002 PHE Q 112 TRP 0.045 0.002 TRP H 148 HIS 0.009 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (23863) covalent geometry : angle 0.83962 / 0.42 (32478) hydrogen bonds : bond 0.04816 / 3.10 ( 1320) hydrogen bonds : angle 5.98122 / 4.11 ( 3861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 444 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.6916 (ptm160) cc_final: 0.6658 (ptm-80) REVERT: H 45 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7183 (tpt170) REVERT: H 60 MET cc_start: 0.8397 (mmt) cc_final: 0.8189 (mmm) REVERT: H 65 GLU cc_start: 0.8323 (tt0) cc_final: 0.7740 (tm-30) REVERT: H 106 MET cc_start: 0.7759 (mmm) cc_final: 0.7516 (mmm) REVERT: H 162 LEU cc_start: 0.8970 (tp) cc_final: 0.8743 (tp) REVERT: I 132 CYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6631 (p) REVERT: I 214 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8815 (t) REVERT: I 428 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8664 (tt) REVERT: I 566 GLU cc_start: 0.7807 (tt0) cc_final: 0.7527 (tt0) REVERT: I 604 CYS cc_start: 0.6405 (OUTLIER) cc_final: 0.6071 (t) REVERT: K 26 ARG cc_start: 0.7780 (tmm160) cc_final: 0.7364 (tmm160) REVERT: K 223 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6863 (pp) REVERT: L 30 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.6820 (tpp80) REVERT: L 319 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6656 (pptt) REVERT: M 76 TYR cc_start: 0.8552 (t80) cc_final: 0.8345 (t80) REVERT: N 69 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8268 (tt) REVERT: O 187 TYR cc_start: 0.8704 (m-80) cc_final: 0.8297 (m-80) REVERT: O 289 ARG cc_start: 0.6191 (ttp80) cc_final: 0.5904 (ttp80) REVERT: O 296 MET cc_start: 0.6299 (mmm) cc_final: 0.5296 (mmm) REVERT: P 113 MET cc_start: 0.4735 (mpp) cc_final: 0.2841 (mmt) REVERT: S 40 MET cc_start: 0.4381 (tpp) cc_final: 0.4094 (tpp) REVERT: S 52 GLU cc_start: 0.7970 (pp20) cc_final: 0.7765 (pp20) REVERT: S 94 LYS cc_start: 0.8626 (pptt) cc_final: 0.8117 (tppt) REVERT: T 485 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8392 (pptt) REVERT: X 20 HIS cc_start: 0.7670 (m90) cc_final: 0.7371 (m-70) REVERT: Q 93 MET cc_start: 0.7917 (mtm) cc_final: 0.7471 (mmm) REVERT: Q 131 MET cc_start: 0.7251 (pmm) cc_final: 0.6658 (pmm) REVERT: Q 185 ILE cc_start: 0.8269 (mp) cc_final: 0.7724 (mm) REVERT: Q 196 ARG cc_start: 0.4244 (OUTLIER) cc_final: 0.3906 (mmp80) outliers start: 120 outliers final: 79 residues processed: 523 average time/residue: 0.1628 time to fit residues: 132.5123 Evaluate side-chains 495 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 405 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 451 CYS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 322 ILE Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 189 GLU Chi-restraints excluded: chain Q residue 196 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 ASN L 71 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.160312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.129311 restraints weight = 54242.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.127460 restraints weight = 46826.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.128263 restraints weight = 38245.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.128794 restraints weight = 31174.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.128875 restraints weight = 29018.326| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23863 Z= 0.183 Angle : 0.874 14.579 32478 Z= 0.435 Chirality : 0.047 0.366 3799 Planarity : 0.005 0.059 3940 Dihedral : 14.423 87.417 3575 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.92 % Favored : 91.72 % Rotamer: Outliers : 4.65 % Allowed : 28.81 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.15), residues: 2814 helix: -0.24 (0.12), residues: 1749 sheet: -2.92 (0.36), residues: 160 loop : -2.83 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG Q 147 TYR 0.057 0.002 TYR S 95 PHE 0.041 0.002 PHE Q 112 TRP 0.044 0.002 TRP N 28 HIS 0.009 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (23863) covalent geometry : angle 0.87429 / 0.43 (32478) hydrogen bonds : bond 0.04849 / 3.12 ( 1320) hydrogen bonds : angle 5.90208 / 4.06 ( 3861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 428 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.6754 (ptm160) cc_final: 0.6532 (ptm-80) REVERT: H 65 GLU cc_start: 0.8254 (tt0) cc_final: 0.7705 (tm-30) REVERT: H 106 MET cc_start: 0.7701 (mmm) cc_final: 0.7474 (mmm) REVERT: H 162 LEU cc_start: 0.8943 (tp) cc_final: 0.8714 (tp) REVERT: I 132 CYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6294 (p) REVERT: I 428 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8602 (tt) REVERT: I 566 GLU cc_start: 0.7762 (tt0) cc_final: 0.7488 (tt0) REVERT: I 604 CYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5679 (t) REVERT: I 642 HIS cc_start: 0.6304 (t-170) cc_final: 0.6080 (t70) REVERT: K 223 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6859 (pp) REVERT: L 30 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6759 (tpp80) REVERT: L 57 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6340 (pt0) REVERT: L 205 ASP cc_start: 0.8238 (t0) cc_final: 0.7890 (t0) REVERT: L 319 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6614 (pptt) REVERT: O 187 TYR cc_start: 0.8635 (m-80) cc_final: 0.8301 (m-80) REVERT: O 196 ARG cc_start: 0.7846 (tpm170) cc_final: 0.7517 (tpm170) REVERT: O 296 MET cc_start: 0.6185 (mmm) cc_final: 0.5302 (mmm) REVERT: P 113 MET cc_start: 0.4588 (mpp) cc_final: 0.2634 (mmt) REVERT: S 40 MET cc_start: 0.4393 (tpp) cc_final: 0.4178 (tpp) REVERT: S 94 LYS cc_start: 0.8551 (pptt) cc_final: 0.8079 (tppt) REVERT: T 485 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8541 (pptt) REVERT: X 20 HIS cc_start: 0.7545 (m90) cc_final: 0.7237 (m-70) REVERT: X 43 LYS cc_start: 0.7888 (tttp) cc_final: 0.7501 (mttt) REVERT: X 74 LEU cc_start: 0.8470 (mt) cc_final: 0.8236 (tp) REVERT: Q 93 MET cc_start: 0.7832 (mtm) cc_final: 0.7398 (mmm) REVERT: Q 131 MET cc_start: 0.6953 (pmm) cc_final: 0.6480 (pmm) REVERT: Q 182 LYS cc_start: 0.7958 (pptt) cc_final: 0.7318 (pptt) outliers start: 108 outliers final: 88 residues processed: 505 average time/residue: 0.1575 time to fit residues: 124.1335 Evaluate side-chains 500 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 404 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 174 PHE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 451 CYS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 236 ASP Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 325 HIS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 294 LEU Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 484 GLU Chi-restraints excluded: chain T residue 485 LYS Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 163 ASP Chi-restraints excluded: chain Q residue 189 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 270 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** o 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.159285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.127576 restraints weight = 54140.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.125513 restraints weight = 56204.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.127144 restraints weight = 47755.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.127352 restraints weight = 35721.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.127476 restraints weight = 33572.711| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 23863 Z= 0.229 Angle : 0.902 14.402 32478 Z= 0.452 Chirality : 0.049 0.397 3799 Planarity : 0.005 0.066 3940 Dihedral : 14.366 86.867 3575 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.39 % Favored : 91.29 % Rotamer: Outliers : 4.52 % Allowed : 29.29 % Favored : 66.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2814 helix: -0.19 (0.12), residues: 1757 sheet: -3.01 (0.35), residues: 161 loop : -2.86 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 147 TYR 0.037 0.002 TYR S 95 PHE 0.042 0.002 PHE Q 112 TRP 0.041 0.003 TRP H 148 HIS 0.020 0.002 HIS Q 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (23863) covalent geometry : angle 0.90196 / 0.45 (32478) hydrogen bonds : bond 0.04956 / 3.21 ( 1320) hydrogen bonds : angle 5.92124 / 4.07 ( 3861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 408 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 23 ARG cc_start: 0.7029 (ptm160) cc_final: 0.6754 (ptm-80) REVERT: H 141 MET cc_start: 0.6289 (ptt) cc_final: 0.6080 (ptt) REVERT: I 132 CYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6462 (p) REVERT: I 428 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8686 (tt) REVERT: I 566 GLU cc_start: 0.7808 (tt0) cc_final: 0.7519 (tt0) REVERT: I 604 CYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5671 (t) REVERT: K 101 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7698 (tpp80) REVERT: K 223 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7035 (pp) REVERT: L 30 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.6833 (tpp80) REVERT: L 319 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6773 (pptt) REVERT: O 187 TYR cc_start: 0.8596 (m-80) cc_final: 0.8256 (m-80) REVERT: O 196 ARG cc_start: 0.7871 (tpm170) cc_final: 0.7538 (tpm170) REVERT: O 296 MET cc_start: 0.6066 (mmm) cc_final: 0.5188 (mmm) REVERT: P 113 MET cc_start: 0.4586 (mpp) cc_final: 0.2641 (mmt) REVERT: S 94 LYS cc_start: 0.8534 (pptt) cc_final: 0.8031 (tppt) REVERT: T 513 GLU cc_start: 0.8468 (pm20) cc_final: 0.8117 (pm20) REVERT: X 20 HIS cc_start: 0.7438 (m90) cc_final: 0.7122 (m-70) REVERT: X 74 LEU cc_start: 0.8431 (mt) cc_final: 0.8167 (tp) REVERT: Q 93 MET cc_start: 0.7745 (mtm) cc_final: 0.7365 (mmm) REVERT: Q 131 MET cc_start: 0.6933 (pmm) cc_final: 0.6506 (pmm) outliers start: 105 outliers final: 83 residues processed: 484 average time/residue: 0.1524 time to fit residues: 114.3488 Evaluate side-chains 476 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 387 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 100 TRP Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 174 PHE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 451 CYS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 582 LEU Chi-restraints excluded: chain I residue 599 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain I residue 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 66 CYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 217 GLU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 262 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 319 LYS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 HIS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 253 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 193 ASP Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain S residue 13 PHE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 470 TYR Chi-restraints excluded: chain T residue 477 ARG Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 189 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 199 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** o 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.159685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.127354 restraints weight = 53900.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.125960 restraints weight = 54045.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.127037 restraints weight = 47381.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.127428 restraints weight = 37413.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.127843 restraints weight = 36363.988| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 23863 Z= 0.201 Angle : 0.902 14.400 32478 Z= 0.448 Chirality : 0.048 0.261 3799 Planarity : 0.005 0.071 3940 Dihedral : 14.327 86.733 3575 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.17 % Favored : 91.51 % Rotamer: Outliers : 4.39 % Allowed : 29.41 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.15), residues: 2814 helix: -0.18 (0.12), residues: 1747 sheet: -2.95 (0.35), residues: 161 loop : -2.87 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 289 TYR 0.036 0.002 TYR S 95 PHE 0.042 0.002 PHE Q 112 TRP 0.040 0.002 TRP H 148 HIS 0.013 0.001 HIS K 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (23863) covalent geometry : angle 0.90185 / 0.45 (32478) hydrogen bonds : bond 0.04820 / 3.11 ( 1320) hydrogen bonds : angle 5.88361 / 4.04 ( 3861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.59 seconds wall clock time: 72 minutes 49.74 seconds (4369.74 seconds total)