Starting phenix.real_space_refine on Sat Jul 4 20:18:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xhn_33196/07_2026/7xhn_33196.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xhn_33196/07_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_33196/07_2026/7xhn_33196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xhn_33196/07_2026/7xhn_33196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xhn_33196/07_2026/7xhn_33196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xhn_33196/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.99, per 1000 atoms: 0.17 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.68 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: 3.48 Time building geometry restraints manager: 2.30 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: 2.600 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.210 Find NCS groups from input model: 0.120 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- 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 1.26615 / 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 : 0.662 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: 0.1538 time to fit residues: 104.6559 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 : 0.881 ------------------------------------------------------------------------------- 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 54 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN L 71 GLN L 290 HIS M 125 GLN ** 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.159922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.127710 restraints weight = 54583.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125453 restraints weight = 51865.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.127247 restraints weight = 42379.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.127475 restraints weight = 33182.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.127525 restraints weight = 31580.487| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23863 Z= 0.224 Angle : 0.863 15.854 32478 Z= 0.442 Chirality : 0.047 0.304 3799 Planarity : 0.006 0.077 3940 Dihedral : 15.079 87.183 3609 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.74 % Favored : 90.83 % Rotamer: Outliers : 4.78 % Allowed : 24.98 % Favored : 70.24 % 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: -1.08 (0.12), residues: 1710 sheet: -3.86 (0.30), residues: 188 loop : -2.87 (0.20), residues: 916 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 0.037 0.002 PHE I 734 TRP 0.037 0.003 TRP H 148 HIS 0.019 0.002 HIS Q 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (23863) covalent geometry : angle 0.86346 / 0.44 (32478) hydrogen bonds : bond 0.06467 / 4.15 ( 1320) hydrogen bonds : angle 6.97702 / 4.81 ( 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 578 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 467 time to evaluate : 0.648 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: o 23 ARG cc_start: 0.6769 (ptm160) cc_final: 0.6472 (ptm-80) REVERT: H 106 MET cc_start: 0.7813 (mmm) cc_final: 0.7473 (mmm) REVERT: H 142 LYS cc_start: 0.8565 (mttt) cc_final: 0.7870 (mttt) REVERT: H 189 MET cc_start: 0.6272 (mpp) cc_final: 0.5281 (mpp) REVERT: I 132 CYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6769 (p) REVERT: I 214 VAL cc_start: 0.9262 (t) cc_final: 0.9026 (t) REVERT: I 440 TYR cc_start: 0.8182 (m-80) cc_final: 0.7971 (m-80) REVERT: I 474 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8244 (tt) REVERT: I 570 ASP cc_start: 0.7010 (p0) cc_final: 0.6605 (p0) REVERT: I 691 TYR cc_start: 0.6620 (m-80) cc_final: 0.6292 (m-80) REVERT: I 726 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6776 (mm-40) REVERT: K 26 ARG cc_start: 0.7810 (tmm160) cc_final: 0.7387 (tmm160) REVERT: K 27 GLU cc_start: 0.7786 (pm20) cc_final: 0.7411 (pm20) REVERT: L 31 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5936 (mm) REVERT: L 205 ASP cc_start: 0.8092 (t0) cc_final: 0.7852 (t0) REVERT: M 93 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8035 (t80) REVERT: N 169 ARG cc_start: 0.6761 (mtm180) cc_final: 0.6279 (mtm180) REVERT: N 171 ASN cc_start: 0.7473 (p0) cc_final: 0.7184 (p0) REVERT: N 191 MET cc_start: 0.8395 (tpp) cc_final: 0.7929 (ttt) REVERT: S 19 LEU cc_start: 0.8652 (mt) cc_final: 0.8094 (mt) REVERT: X 74 LEU cc_start: 0.9015 (mm) cc_final: 0.8709 (pp) outliers start: 111 outliers final: 52 residues processed: 539 average time/residue: 0.1506 time to fit residues: 124.9445 Evaluate side-chains 474 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 417 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 93 PHE 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 126 ILE 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 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: 2.9990 chunk 162 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 257 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 554 ASN I 726 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** 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 185 ASN ** O 193 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.159889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.126696 restraints weight = 54368.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.124994 restraints weight = 43926.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.126216 restraints weight = 36988.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.126588 restraints weight = 30763.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.126782 restraints weight = 26262.323| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23863 Z= 0.189 Angle : 0.813 17.460 32478 Z= 0.414 Chirality : 0.046 0.210 3799 Planarity : 0.005 0.077 3940 Dihedral : 14.820 86.672 3584 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.35 % Favored : 91.22 % Rotamer: Outliers : 4.82 % Allowed : 24.63 % 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: -2.62 (0.15), residues: 2814 helix: -0.88 (0.12), residues: 1731 sheet: -3.56 (0.32), residues: 183 loop : -2.85 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 52 TYR 0.030 0.002 TYR T 470 PHE 0.038 0.002 PHE Q 112 TRP 0.032 0.002 TRP H 148 HIS 0.011 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (23863) covalent geometry : angle 0.81342 / 0.41 (32478) hydrogen bonds : bond 0.05756 / 3.70 ( 1320) hydrogen bonds : angle 6.58764 / 4.54 ( 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 565 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 453 time to evaluate : 0.753 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: o 23 ARG cc_start: 0.6318 (ptm160) cc_final: 0.6069 (ptm-80) REVERT: H 189 MET cc_start: 0.6182 (mpp) cc_final: 0.5681 (mmp) REVERT: I 73 PHE cc_start: 0.4179 (m-80) cc_final: 0.3604 (m-10) REVERT: I 132 CYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7005 (p) REVERT: I 167 TRP cc_start: 0.6682 (t60) cc_final: 0.6061 (t60) REVERT: I 214 VAL cc_start: 0.9194 (t) cc_final: 0.8944 (t) REVERT: I 456 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8625 (mp) REVERT: I 491 CYS cc_start: 0.7945 (m) cc_final: 0.7722 (m) REVERT: I 570 ASP cc_start: 0.6949 (p0) cc_final: 0.6600 (p0) REVERT: I 726 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7077 (tp-100) REVERT: L 31 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.4664 (mm) REVERT: L 205 ASP cc_start: 0.8111 (t0) cc_final: 0.7758 (t0) REVERT: L 260 ASP cc_start: 0.7683 (m-30) cc_final: 0.7419 (m-30) REVERT: L 319 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6846 (pptt) REVERT: M 76 TYR cc_start: 0.8545 (t80) cc_final: 0.7851 (t80) REVERT: M 79 GLN cc_start: 0.7665 (mp10) cc_final: 0.7373 (mp10) REVERT: N 171 ASN cc_start: 0.7176 (p0) cc_final: 0.6923 (p0) REVERT: N 191 MET cc_start: 0.8197 (tpp) cc_final: 0.7808 (ttm) REVERT: O 174 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.5937 (tm-30) REVERT: O 181 CYS cc_start: 0.8000 (m) cc_final: 0.7794 (m) REVERT: O 212 ASN cc_start: 0.7664 (m-40) cc_final: 0.7299 (m-40) REVERT: O 296 MET cc_start: 0.6667 (mmm) cc_final: 0.5487 (mmm) REVERT: P 136 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7098 (p) REVERT: S 52 GLU cc_start: 0.8570 (pt0) cc_final: 0.8327 (pp20) REVERT: S 53 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.7848 (mm) REVERT: T 485 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8120 (pttp) REVERT: T 519 MET cc_start: 0.8276 (mtt) cc_final: 0.7954 (mtm) REVERT: W 52 HIS cc_start: 0.7831 (t70) cc_final: 0.7426 (t70) REVERT: X 38 MET cc_start: 0.6286 (tmm) cc_final: 0.5887 (tmm) REVERT: Q 131 MET cc_start: 0.7204 (pmm) cc_final: 0.6925 (pmm) outliers start: 112 outliers final: 56 residues processed: 529 average time/residue: 0.1444 time to fit residues: 118.2999 Evaluate side-chains 483 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 418 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 141 THR Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 141 ASP Chi-restraints excluded: chain O residue 174 GLN Chi-restraints excluded: chain O residue 185 ASN 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 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 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: 3.9990 chunk 244 optimal weight: 50.0000 chunk 201 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 242 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 115 ASN ** I 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 210 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.157379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130498 restraints weight = 54083.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.126124 restraints weight = 77159.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.124189 restraints weight = 51954.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.123901 restraints weight = 47615.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.124199 restraints weight = 39946.174| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 23863 Z= 0.304 Angle : 0.875 14.954 32478 Z= 0.444 Chirality : 0.048 0.297 3799 Planarity : 0.006 0.086 3940 Dihedral : 14.781 86.438 3580 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.10 % Favored : 90.48 % Rotamer: Outliers : 6.03 % Allowed : 25.06 % Favored : 68.91 % 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: -2.44 (0.15), residues: 2814 helix: -0.71 (0.12), residues: 1738 sheet: -3.58 (0.32), residues: 186 loop : -2.83 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 147 TYR 0.038 0.002 TYR T 470 PHE 0.032 0.003 PHE Q 112 TRP 0.032 0.002 TRP N 28 HIS 0.010 0.002 HIS P 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.30 (23863) covalent geometry : angle 0.87485 / 0.44 (32478) hydrogen bonds : bond 0.05790 / 3.74 ( 1320) hydrogen bonds : angle 6.42305 / 4.44 ( 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 561 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 421 time to evaluate : 0.874 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: 0.6890 (ptm160) cc_final: 0.6605 (ptm-80) REVERT: H 106 MET cc_start: 0.7950 (mmm) cc_final: 0.7577 (mmm) REVERT: H 189 MET cc_start: 0.6611 (mpp) cc_final: 0.6135 (mmt) REVERT: I 132 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6565 (p) REVERT: I 214 VAL cc_start: 0.9275 (t) cc_final: 0.9040 (t) REVERT: I 643 TYR cc_start: 0.8026 (m-10) cc_final: 0.7588 (m-10) REVERT: I 647 MET cc_start: 0.7747 (ppp) cc_final: 0.7518 (ppp) REVERT: K 45 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6337 (pt) REVERT: K 80 GLU cc_start: 0.6052 (tp30) cc_final: 0.5793 (tp30) REVERT: K 223 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6940 (pp) REVERT: L 205 ASP cc_start: 0.8257 (t0) cc_final: 0.7798 (t0) REVERT: L 319 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6615 (pptt) REVERT: M 75 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8131 (ttpt) REVERT: M 79 GLN cc_start: 0.7876 (mt0) cc_final: 0.7493 (mp10) REVERT: M 170 ARG cc_start: 0.7355 (ttm110) cc_final: 0.7099 (ttm110) REVERT: N 69 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8593 (tt) REVERT: N 148 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8527 (mtpt) REVERT: N 191 MET cc_start: 0.8443 (tpp) cc_final: 0.7958 (ttm) REVERT: O 181 CYS cc_start: 0.7872 (m) cc_final: 0.7643 (m) REVERT: O 212 ASN cc_start: 0.7784 (m-40) cc_final: 0.7557 (m-40) REVERT: O 296 MET cc_start: 0.6738 (mmm) cc_final: 0.5382 (mmm) REVERT: P 136 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.7108 (p) REVERT: S 52 GLU cc_start: 0.8617 (pt0) cc_final: 0.8367 (pp20) REVERT: S 53 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7514 (mm) REVERT: T 485 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8055 (pttp) REVERT: W 52 HIS cc_start: 0.8273 (t70) cc_final: 0.7450 (t70) REVERT: W 83 LEU cc_start: 0.8634 (pp) cc_final: 0.8183 (tt) REVERT: X 38 MET cc_start: 0.6649 (tmm) cc_final: 0.6353 (tmm) REVERT: Q 131 MET cc_start: 0.7185 (pmm) cc_final: 0.6920 (pmm) REVERT: Q 196 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.3634 (mmp80) outliers start: 140 outliers final: 77 residues processed: 517 average time/residue: 0.1506 time to fit residues: 120.0310 Evaluate side-chains 489 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 401 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 443 LEU Chi-restraints excluded: chain I residue 445 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 728 LEU Chi-restraints excluded: chain I residue 731 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 180 LEU 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 L residue 31 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 322 ILE 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 102 THR 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 16 ILE Chi-restraints excluded: chain N residue 20 GLU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 148 LYS Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 108 TYR 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 150 ILE Chi-restraints excluded: chain O residue 185 ASN 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 36 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 262 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 249 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** K 249 ASN L 71 GLN ** 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** ** 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** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS Q 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.158634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.125470 restraints weight = 53734.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.123039 restraints weight = 45709.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.124254 restraints weight = 39189.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.124660 restraints weight = 32383.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.124679 restraints weight = 31385.783| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 23863 Z= 0.209 Angle : 0.838 15.442 32478 Z= 0.419 Chirality : 0.047 0.238 3799 Planarity : 0.005 0.070 3940 Dihedral : 14.756 87.276 3578 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.49 % Favored : 91.12 % Rotamer: Outliers : 5.64 % Allowed : 25.93 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.15), residues: 2814 helix: -0.62 (0.12), residues: 1742 sheet: -3.45 (0.32), residues: 184 loop : -2.83 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 147 TYR 0.031 0.002 TYR P 179 PHE 0.044 0.002 PHE Q 112 TRP 0.044 0.002 TRP N 28 HIS 0.011 0.001 HIS K 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (23863) covalent geometry : angle 0.83818 / 0.42 (32478) hydrogen bonds : bond 0.05313 / 3.43 ( 1320) hydrogen bonds : angle 6.26064 / 4.32 ( 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 556 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 425 time to evaluate : 0.832 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: 0.6775 (ptm160) cc_final: 0.6503 (ptm-80) REVERT: I 132 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6277 (p) REVERT: I 214 VAL cc_start: 0.9186 (t) cc_final: 0.8890 (t) REVERT: I 229 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.6093 (mmm) REVERT: I 428 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8718 (tt) REVERT: I 604 CYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6125 (t) REVERT: I 643 TYR cc_start: 0.7738 (m-10) cc_final: 0.7504 (m-10) REVERT: I 647 MET cc_start: 0.7607 (ppp) cc_final: 0.7338 (ppp) REVERT: K 67 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7881 (mm) REVERT: K 223 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6887 (pp) REVERT: L 85 TYR cc_start: 0.7245 (m-80) cc_final: 0.7030 (m-80) REVERT: L 205 ASP cc_start: 0.8235 (t0) cc_final: 0.7783 (t0) REVERT: L 319 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6755 (pptt) REVERT: M 75 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8639 (ttpt) REVERT: M 170 ARG cc_start: 0.7358 (ttm110) cc_final: 0.7087 (ttm110) REVERT: N 28 TRP cc_start: 0.7378 (p-90) cc_final: 0.7092 (p-90) REVERT: N 69 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8388 (tt) REVERT: N 148 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8472 (mtpt) REVERT: N 191 MET cc_start: 0.8305 (tpp) cc_final: 0.7823 (ttm) REVERT: O 296 MET cc_start: 0.6500 (mmm) cc_final: 0.5266 (mmm) REVERT: T 484 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7592 (mp0) REVERT: T 536 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7429 (mt-10) REVERT: W 83 LEU cc_start: 0.8401 (pp) cc_final: 0.8005 (tt) REVERT: Q 93 MET cc_start: 0.8059 (mtm) cc_final: 0.7665 (mmm) REVERT: Q 131 MET cc_start: 0.7150 (pmm) cc_final: 0.6819 (pmm) REVERT: Q 196 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.3685 (mmp80) outliers start: 131 outliers final: 74 residues processed: 516 average time/residue: 0.1539 time to fit residues: 123.4269 Evaluate side-chains 483 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 398 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 188 SER 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 174 PHE 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 604 CYS Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain I residue 695 PHE 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 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 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 159 THR 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 111 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 148 LYS Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 140 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 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 137 ASP Chi-restraints excluded: chain P residue 222 TRP Chi-restraints excluded: chain S residue 13 PHE 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 36 GLN Chi-restraints excluded: chain X residue 67 VAL 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: 0.8980 chunk 178 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS K 54 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN L 71 GLN ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.157879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.130910 restraints weight = 54245.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125468 restraints weight = 67153.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.123491 restraints weight = 49824.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.123959 restraints weight = 43472.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.124223 restraints weight = 35466.012| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23863 Z= 0.226 Angle : 0.845 15.125 32478 Z= 0.423 Chirality : 0.047 0.265 3799 Planarity : 0.005 0.092 3940 Dihedral : 14.684 87.336 3576 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.64 % Favored : 90.97 % Rotamer: Outliers : 5.77 % Allowed : 26.44 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.15), residues: 2814 helix: -0.52 (0.12), residues: 1744 sheet: -3.43 (0.33), residues: 174 loop : -2.85 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 147 TYR 0.033 0.002 TYR T 470 PHE 0.043 0.002 PHE Q 112 TRP 0.033 0.002 TRP N 28 HIS 0.020 0.002 HIS Q 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (23863) covalent geometry : angle 0.84539 / 0.42 (32478) hydrogen bonds : bond 0.05214 / 3.37 ( 1320) hydrogen bonds : angle 6.14388 / 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 551 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 417 time to evaluate : 1.049 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: 0.6842 (ptm160) cc_final: 0.6584 (ptm-80) REVERT: H 106 MET cc_start: 0.7932 (mmm) cc_final: 0.7595 (mmm) REVERT: I 132 CYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6422 (p) REVERT: I 214 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8929 (t) REVERT: I 229 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.6112 (mmm) REVERT: I 474 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8233 (tt) REVERT: I 604 CYS cc_start: 0.6313 (OUTLIER) cc_final: 0.5914 (t) REVERT: I 642 HIS cc_start: 0.6853 (t-170) cc_final: 0.6443 (t-170) REVERT: I 643 TYR cc_start: 0.7820 (m-10) cc_final: 0.7460 (m-10) REVERT: I 647 MET cc_start: 0.7748 (ppp) cc_final: 0.7538 (ppp) REVERT: I 726 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6883 (mp10) REVERT: K 30 GLU cc_start: 0.8929 (pt0) cc_final: 0.8470 (pp20) REVERT: K 223 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6986 (pp) REVERT: L 30 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.6919 (tpp80) REVERT: L 71 GLN cc_start: 0.8273 (tp-100) cc_final: 0.8048 (tp40) REVERT: L 205 ASP cc_start: 0.8020 (t0) cc_final: 0.7794 (t0) REVERT: L 319 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6716 (pptt) REVERT: M 44 LEU cc_start: 0.8250 (mt) cc_final: 0.7943 (mt) REVERT: M 170 ARG cc_start: 0.7412 (ttm110) cc_final: 0.7140 (ttm110) REVERT: N 28 TRP cc_start: 0.7240 (p-90) cc_final: 0.6970 (p-90) REVERT: N 69 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8370 (tt) REVERT: S 40 MET cc_start: 0.4645 (tpp) cc_final: 0.4343 (tpp) REVERT: S 94 LYS cc_start: 0.8739 (pptt) cc_final: 0.8263 (tppt) REVERT: T 485 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8535 (pptt) REVERT: W 83 LEU cc_start: 0.8542 (pp) cc_final: 0.8154 (tt) REVERT: X 20 HIS cc_start: 0.7911 (m90) cc_final: 0.7546 (m-70) REVERT: X 43 LYS cc_start: 0.7973 (tttp) cc_final: 0.7620 (mttt) REVERT: X 45 PHE cc_start: 0.8494 (t80) cc_final: 0.8236 (t80) REVERT: X 81 PHE cc_start: 0.6196 (t80) cc_final: 0.5795 (t80) REVERT: Q 93 MET cc_start: 0.8271 (mtm) cc_final: 0.7789 (mmm) REVERT: Q 131 MET cc_start: 0.7236 (pmm) cc_final: 0.6941 (pmm) REVERT: Q 196 ARG cc_start: 0.4774 (OUTLIER) cc_final: 0.3938 (mmp80) outliers start: 134 outliers final: 89 residues processed: 513 average time/residue: 0.1562 time to fit residues: 123.9966 Evaluate side-chains 495 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 394 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL 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 173 ASP Chi-restraints excluded: chain I residue 174 PHE Chi-restraints excluded: chain I residue 214 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 443 LEU Chi-restraints excluded: chain I residue 451 CYS 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 604 CYS Chi-restraints excluded: chain I residue 685 HIS Chi-restraints excluded: chain I residue 689 LEU 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 110 THR Chi-restraints excluded: chain K residue 118 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 232 VAL 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 159 THR 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 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 322 ILE 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 30 PHE Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain O residue 104 ILE Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 140 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 114 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 137 ASP Chi-restraints excluded: chain P residue 179 TYR 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 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 36 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 79 LEU 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: 0.6980 chunk 255 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 274 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 30 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 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** P 110 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.158713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.126818 restraints weight = 54160.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.125225 restraints weight = 48486.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.126531 restraints weight = 47201.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.126751 restraints weight = 35117.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.126853 restraints weight = 31065.100| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23863 Z= 0.198 Angle : 0.847 14.538 32478 Z= 0.421 Chirality : 0.047 0.311 3799 Planarity : 0.005 0.064 3940 Dihedral : 14.593 87.682 3576 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.46 % Favored : 91.15 % Rotamer: Outliers : 5.47 % Allowed : 27.22 % Favored : 67.31 % 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: -2.09 (0.15), residues: 2814 helix: -0.40 (0.12), residues: 1737 sheet: -3.40 (0.34), residues: 161 loop : -2.81 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 289 TYR 0.033 0.002 TYR I 722 PHE 0.090 0.002 PHE K 97 TRP 0.032 0.002 TRP H 148 HIS 0.010 0.001 HIS W 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (23863) covalent geometry : angle 0.84709 / 0.42 (32478) hydrogen bonds : bond 0.05016 / 3.24 ( 1320) hydrogen bonds : angle 6.04520 / 4.17 ( 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 550 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 423 time to evaluate : 0.687 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: o 23 ARG cc_start: 0.6858 (ptm160) cc_final: 0.6584 (ptm-80) REVERT: H 60 MET cc_start: 0.8376 (mmt) cc_final: 0.8170 (mmm) REVERT: H 106 MET cc_start: 0.7720 (mmm) cc_final: 0.7515 (mmm) REVERT: H 115 ASN cc_start: 0.8385 (m110) cc_final: 0.8126 (p0) REVERT: H 137 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8082 (t0) REVERT: H 142 LYS cc_start: 0.8159 (mttt) cc_final: 0.7772 (mttt) REVERT: I 111 ILE cc_start: 0.7280 (mm) cc_final: 0.7045 (mm) REVERT: I 132 CYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5792 (p) REVERT: I 214 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8880 (t) REVERT: I 428 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8745 (tt) REVERT: I 566 GLU cc_start: 0.7944 (tt0) cc_final: 0.7654 (tt0) REVERT: I 604 CYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5982 (t) REVERT: I 642 HIS cc_start: 0.6598 (t-170) cc_final: 0.6275 (t-170) REVERT: I 643 TYR cc_start: 0.7776 (m-10) cc_final: 0.7502 (m-10) REVERT: I 726 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6983 (mp10) REVERT: K 26 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7577 (tmm160) REVERT: K 27 GLU cc_start: 0.7623 (pm20) cc_final: 0.7412 (pm20) REVERT: K 30 GLU cc_start: 0.8668 (pt0) cc_final: 0.8451 (pp20) REVERT: K 31 MET cc_start: 0.8044 (mtt) cc_final: 0.7803 (mtt) REVERT: K 223 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7106 (pp) REVERT: L 30 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.6930 (tpp80) REVERT: L 71 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8021 (tp40) REVERT: L 205 ASP cc_start: 0.8123 (t0) cc_final: 0.7900 (t0) REVERT: L 319 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6632 (pptt) REVERT: M 44 LEU cc_start: 0.8229 (mt) cc_final: 0.7968 (mt) REVERT: N 69 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8256 (tt) REVERT: O 296 MET cc_start: 0.6368 (mmm) cc_final: 0.6160 (tmm) REVERT: P 113 MET cc_start: 0.4406 (mpp) cc_final: 0.2500 (mmt) REVERT: S 40 MET cc_start: 0.4496 (tpp) cc_final: 0.4170 (tpp) REVERT: S 52 GLU cc_start: 0.7876 (pp20) cc_final: 0.7574 (pp20) REVERT: T 484 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7697 (mm-30) REVERT: T 485 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8530 (pptt) REVERT: W 83 LEU cc_start: 0.8370 (pp) cc_final: 0.8086 (tt) REVERT: X 20 HIS cc_start: 0.7543 (m90) cc_final: 0.7202 (m-70) REVERT: X 43 LYS cc_start: 0.7787 (tttp) cc_final: 0.7532 (mttt) REVERT: Q 93 MET cc_start: 0.7883 (mtm) cc_final: 0.7466 (mmm) REVERT: Q 131 MET cc_start: 0.7163 (pmm) cc_final: 0.6864 (pmm) REVERT: Q 196 ARG cc_start: 0.4361 (OUTLIER) cc_final: 0.3885 (mmp80) outliers start: 127 outliers final: 88 residues processed: 510 average time/residue: 0.1586 time to fit residues: 125.5012 Evaluate side-chains 501 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 401 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain H residue 148 TRP Chi-restraints excluded: chain H residue 188 SER 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 214 VAL 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 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 110 THR Chi-restraints excluded: chain K residue 118 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 232 VAL 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 159 THR 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 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 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 114 ARG 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 30 PHE Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 104 ILE Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE 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 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 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 63 CYS 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 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: 2.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 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 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 ASN I 602 GLN I 726 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.159298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.127279 restraints weight = 54114.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.125166 restraints weight = 49465.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.126491 restraints weight = 42139.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.126778 restraints weight = 33599.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.126923 restraints weight = 32081.606| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23863 Z= 0.178 Angle : 0.843 15.688 32478 Z= 0.420 Chirality : 0.046 0.272 3799 Planarity : 0.005 0.063 3940 Dihedral : 14.540 87.799 3576 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.10 % Favored : 91.58 % Rotamer: Outliers : 5.43 % Allowed : 27.61 % Favored : 66.97 % 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: -2.02 (0.15), residues: 2814 helix: -0.34 (0.12), residues: 1746 sheet: -3.25 (0.33), residues: 174 loop : -2.84 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 128 TYR 0.031 0.002 TYR T 470 PHE 0.034 0.002 PHE Q 112 TRP 0.053 0.002 TRP N 28 HIS 0.009 0.001 HIS K 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (23863) covalent geometry : angle 0.84258 / 0.42 (32478) hydrogen bonds : bond 0.04861 / 3.13 ( 1320) hydrogen bonds : angle 5.96768 / 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 558 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 432 time to evaluate : 0.962 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: o 23 ARG cc_start: 0.6889 (ptm160) cc_final: 0.6648 (ptm-80) REVERT: H 60 MET cc_start: 0.8385 (mmt) cc_final: 0.8175 (mmm) REVERT: H 106 MET cc_start: 0.7714 (mmm) cc_final: 0.7498 (mmm) REVERT: H 115 ASN cc_start: 0.8386 (m110) cc_final: 0.8141 (p0) REVERT: H 137 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7961 (t0) REVERT: I 112 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4731 (pt) REVERT: I 132 CYS cc_start: 0.6328 (OUTLIER) cc_final: 0.5885 (p) REVERT: I 214 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8823 (t) REVERT: I 566 GLU cc_start: 0.7701 (tt0) cc_final: 0.7401 (tt0) REVERT: I 604 CYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5710 (t) REVERT: I 642 HIS cc_start: 0.6549 (t-170) cc_final: 0.6224 (t-170) REVERT: I 643 TYR cc_start: 0.7649 (m-10) cc_final: 0.7383 (m-10) REVERT: I 691 TYR cc_start: 0.6987 (m-80) cc_final: 0.6581 (m-80) REVERT: K 31 MET cc_start: 0.8031 (mtt) cc_final: 0.7780 (mtt) REVERT: K 223 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7061 (pp) REVERT: L 30 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6850 (tpp80) REVERT: L 71 GLN cc_start: 0.8246 (tp-100) cc_final: 0.8033 (tp40) REVERT: L 205 ASP cc_start: 0.8148 (t0) cc_final: 0.7938 (t0) REVERT: L 319 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6559 (pptt) REVERT: M 44 LEU cc_start: 0.8171 (mt) cc_final: 0.7883 (mt) REVERT: N 69 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8355 (tt) REVERT: N 191 MET cc_start: 0.8271 (tpp) cc_final: 0.7906 (ttm) REVERT: O 187 TYR cc_start: 0.8686 (m-80) cc_final: 0.8251 (m-80) REVERT: O 289 ARG cc_start: 0.5962 (ttp80) cc_final: 0.5679 (ttp80) REVERT: O 296 MET cc_start: 0.6445 (mmm) cc_final: 0.5634 (mmm) REVERT: P 113 MET cc_start: 0.4716 (mpp) cc_final: 0.2636 (mmt) REVERT: S 40 MET cc_start: 0.4480 (tpp) cc_final: 0.4232 (tpp) REVERT: S 94 LYS cc_start: 0.8590 (pptt) cc_final: 0.8092 (tppt) REVERT: T 485 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8559 (pptt) REVERT: W 83 LEU cc_start: 0.8351 (pp) cc_final: 0.8055 (tt) REVERT: X 20 HIS cc_start: 0.7606 (m90) cc_final: 0.7248 (m-70) REVERT: X 43 LYS cc_start: 0.7803 (tttp) cc_final: 0.7542 (mttt) REVERT: Q 93 MET cc_start: 0.7866 (mtm) cc_final: 0.7451 (mmm) REVERT: Q 196 ARG cc_start: 0.4358 (tpt90) cc_final: 0.3939 (mmp80) outliers start: 126 outliers final: 84 residues processed: 521 average time/residue: 0.1595 time to fit residues: 128.8737 Evaluate side-chains 503 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 409 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 215 VAL Chi-restraints excluded: chain I residue 112 LEU 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 214 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 366 VAL 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 118 LEU Chi-restraints excluded: chain K residue 122 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 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 159 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 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 111 SER Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 28 TRP Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE 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 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 T residue 485 LYS Chi-restraints excluded: chain T residue 509 THR 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 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 137 VAL Chi-restraints excluded: chain Q residue 189 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 102 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 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 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** ** 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 ** 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 = 0.4497 r_free = 0.4497 target = 0.159229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134909 restraints weight = 54096.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.126341 restraints weight = 57137.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.125816 restraints weight = 56696.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.126035 restraints weight = 38679.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.126484 restraints weight = 32964.640| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23863 Z= 0.189 Angle : 0.888 14.079 32478 Z= 0.440 Chirality : 0.048 0.534 3799 Planarity : 0.005 0.063 3940 Dihedral : 14.460 87.681 3576 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.14 % Favored : 91.54 % Rotamer: Outliers : 4.61 % Allowed : 28.94 % Favored : 66.45 % 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: -1.92 (0.15), residues: 2814 helix: -0.27 (0.12), residues: 1743 sheet: -2.96 (0.35), residues: 156 loop : -2.84 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 26 TYR 0.022 0.002 TYR I 488 PHE 0.048 0.002 PHE K 97 TRP 0.053 0.003 TRP N 28 HIS 0.009 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (23863) covalent geometry : angle 0.88821 / 0.44 (32478) hydrogen bonds : bond 0.04891 / 3.14 ( 1320) hydrogen bonds : angle 5.92477 / 4.07 ( 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 530 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 423 time to evaluate : 0.805 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: 0.6921 (ptm160) cc_final: 0.6650 (ptm-80) REVERT: H 106 MET cc_start: 0.7745 (mmm) cc_final: 0.7502 (mmm) REVERT: H 115 ASN cc_start: 0.8224 (m110) cc_final: 0.8014 (p0) REVERT: H 137 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8001 (t0) REVERT: I 132 CYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6039 (p) REVERT: I 133 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7393 (pmm) REVERT: I 214 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8856 (t) REVERT: I 604 CYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5706 (t) REVERT: I 642 HIS cc_start: 0.6435 (t-170) cc_final: 0.6133 (t-170) REVERT: I 643 TYR cc_start: 0.7617 (m-10) cc_final: 0.7350 (m-10) REVERT: I 691 TYR cc_start: 0.6986 (m-80) cc_final: 0.6640 (m-80) REVERT: K 223 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7062 (pp) REVERT: L 30 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6818 (tpp80) REVERT: L 319 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6588 (pptt) REVERT: M 44 LEU cc_start: 0.8094 (mt) cc_final: 0.7800 (mt) REVERT: M 114 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8047 (ptm-80) REVERT: N 69 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8335 (tt) REVERT: O 187 TYR cc_start: 0.8604 (m-80) cc_final: 0.8307 (m-80) REVERT: O 296 MET cc_start: 0.6321 (mmm) cc_final: 0.5647 (mmm) REVERT: P 113 MET cc_start: 0.4626 (mpp) cc_final: 0.2562 (mmt) REVERT: S 94 LYS cc_start: 0.8623 (pptt) cc_final: 0.8054 (tppt) REVERT: T 472 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8146 (mmtp) REVERT: T 478 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8554 (tttp) REVERT: W 83 LEU cc_start: 0.8229 (pp) cc_final: 0.7912 (tt) REVERT: X 20 HIS cc_start: 0.7546 (m90) cc_final: 0.7225 (m-70) REVERT: Q 93 MET cc_start: 0.7816 (mtm) cc_final: 0.7382 (mmm) outliers start: 107 outliers final: 82 residues processed: 498 average time/residue: 0.1543 time to fit residues: 118.8202 Evaluate side-chains 488 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 396 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 215 VAL 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 214 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 366 VAL 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 122 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 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 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 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 79 GLN 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 114 ARG Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 28 TRP Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE 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 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 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 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 270 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 241 optimal weight: 0.2980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 39 GLN ** 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 193 GLN ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** 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** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.160293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.135687 restraints weight = 54142.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.127672 restraints weight = 61497.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.129246 restraints weight = 50420.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.128964 restraints weight = 38186.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.129134 restraints weight = 34647.197| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23863 Z= 0.177 Angle : 0.894 14.224 32478 Z= 0.443 Chirality : 0.048 0.492 3799 Planarity : 0.005 0.070 3940 Dihedral : 14.408 87.641 3576 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.89 % Favored : 91.76 % Rotamer: Outliers : 4.09 % Allowed : 29.72 % 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: -1.83 (0.15), residues: 2814 helix: -0.21 (0.12), residues: 1744 sheet: -2.85 (0.36), residues: 157 loop : -2.81 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 194 TYR 0.036 0.002 TYR S 95 PHE 0.037 0.002 PHE Q 112 TRP 0.051 0.003 TRP N 28 HIS 0.015 0.001 HIS Q 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (23863) covalent geometry : angle 0.89386 / 0.44 (32478) hydrogen bonds : bond 0.04831 / 3.11 ( 1320) hydrogen bonds : angle 5.87429 / 4.04 ( 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 515 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 420 time to evaluate : 0.795 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: o 23 ARG cc_start: 0.6850 (ptm160) cc_final: 0.6592 (ptm-80) REVERT: H 106 MET cc_start: 0.7810 (mmm) cc_final: 0.7606 (mmm) REVERT: H 115 ASN cc_start: 0.8219 (m110) cc_final: 0.8016 (p0) REVERT: H 137 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8011 (t0) REVERT: I 132 CYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6185 (p) REVERT: I 604 CYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5685 (t) REVERT: I 642 HIS cc_start: 0.6401 (t-170) cc_final: 0.6090 (t-170) REVERT: I 643 TYR cc_start: 0.7601 (m-10) cc_final: 0.7374 (m-10) REVERT: I 691 TYR cc_start: 0.7014 (m-80) cc_final: 0.6808 (m-80) REVERT: K 223 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7036 (pp) REVERT: L 30 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.6658 (tpp80) REVERT: L 205 ASP cc_start: 0.8391 (t0) cc_final: 0.7987 (t0) REVERT: L 220 TRP cc_start: 0.8196 (m100) cc_final: 0.7674 (m100) REVERT: L 319 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6366 (pptt) REVERT: M 44 LEU cc_start: 0.7915 (mt) cc_final: 0.7596 (mt) REVERT: M 114 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8048 (ptm-80) REVERT: N 69 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8267 (tt) REVERT: O 187 TYR cc_start: 0.8588 (m-80) cc_final: 0.8370 (m-80) REVERT: O 193 GLN cc_start: 0.6619 (tm130) cc_final: 0.6409 (tm-30) REVERT: O 238 LEU cc_start: 0.7943 (mp) cc_final: 0.7511 (tp) REVERT: O 249 ASP cc_start: 0.5887 (t0) cc_final: 0.5667 (t0) REVERT: O 296 MET cc_start: 0.6481 (mmm) cc_final: 0.5713 (mmm) REVERT: P 93 MET cc_start: 0.0076 (ptt) cc_final: -0.0992 (ptt) REVERT: P 113 MET cc_start: 0.4553 (mpp) cc_final: 0.2398 (mmt) REVERT: S 94 LYS cc_start: 0.8609 (pptt) cc_final: 0.8051 (tppt) REVERT: T 478 LYS cc_start: 0.8923 (ptpt) cc_final: 0.8507 (tttp) REVERT: T 495 CYS cc_start: 0.7351 (m) cc_final: 0.7144 (m) REVERT: X 20 HIS cc_start: 0.7490 (m90) cc_final: 0.7235 (m-70) REVERT: X 72 LYS cc_start: 0.8266 (ptpp) cc_final: 0.8040 (mtmm) REVERT: X 74 LEU cc_start: 0.8445 (mt) cc_final: 0.8140 (tp) REVERT: Q 93 MET cc_start: 0.7757 (mtm) cc_final: 0.7364 (mmm) outliers start: 95 outliers final: 80 residues processed: 485 average time/residue: 0.1490 time to fit residues: 112.5117 Evaluate side-chains 480 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 392 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 215 VAL 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 219 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 443 LEU 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 122 LEU Chi-restraints excluded: chain K residue 180 LEU 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 234 VAL 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 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 79 GLN Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 28 TRP Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 108 TYR Chi-restraints excluded: chain O residue 126 ILE 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 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 533 VAL 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 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 42 LEU Chi-restraints excluded: chain X residue 67 VAL 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: 4.9990 chunk 211 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 203 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 ASN I 554 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** ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 493 HIS ** W 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.159309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.126863 restraints weight = 53959.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124769 restraints weight = 48710.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.126079 restraints weight = 42856.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126404 restraints weight = 34811.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.126575 restraints weight = 32826.966| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3937 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= 0.197 Angle : 0.906 14.178 32478 Z= 0.449 Chirality : 0.048 0.503 3799 Planarity : 0.005 0.077 3940 Dihedral : 14.360 87.267 3576 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.24 % Favored : 91.47 % Rotamer: Outliers : 4.13 % Allowed : 29.93 % Favored : 65.93 % 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: -1.79 (0.15), residues: 2814 helix: -0.15 (0.12), residues: 1743 sheet: -2.81 (0.36), residues: 157 loop : -2.86 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 289 TYR 0.030 0.002 TYR S 95 PHE 0.048 0.002 PHE W 50 TRP 0.050 0.003 TRP N 28 HIS 0.015 0.001 HIS K 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (23863) covalent geometry : angle 0.90580 / 0.45 (32478) hydrogen bonds : bond 0.04812 / 3.11 ( 1320) hydrogen bonds : angle 5.84068 / 4.02 ( 3861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3933.39 seconds wall clock time: 69 minutes 11.30 seconds (4151.30 seconds total)