Starting phenix.real_space_refine on Fri Mar 6 04:04:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5s_14336/03_2026/7r5s_14336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5s_14336/03_2026/7r5s_14336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r5s_14336/03_2026/7r5s_14336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5s_14336/03_2026/7r5s_14336.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r5s_14336/03_2026/7r5s_14336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5s_14336/03_2026/7r5s_14336.map" } resolution = 2.83 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= 0.000 sd= 0.001 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 1895 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 82 5.49 5 S 139 5.16 5 C 16926 2.51 5 N 4596 2.21 5 O 5128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 18 Chain: "H" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1652 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5014 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 600} Chain breaks: 5 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 849 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "K" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1922 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2502 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 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: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "N" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2613 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1365 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Chain: "T" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "W" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "S" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} 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: "i" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.20 Number of scatterers: 26871 At special positions: 0 Unit cell: (136.48, 203.014, 196.19, 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 139 16.00 P 82 15.00 O 5128 8.00 N 4596 7.00 C 16926 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 15 sheets defined 64.6% alpha, 9.6% beta 37 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'H' and resid 35 through 65 removed outlier: 3.895A pdb=" N ARG H 39 " --> pdb=" O CYS H 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 114 removed outlier: 4.300A pdb=" N ALA H 80 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 122 removed outlier: 3.935A pdb=" N GLN H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 188 removed outlier: 3.906A pdb=" N LYS H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER H 170 " --> pdb=" O GLN H 166 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP H 185 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU H 186 " --> pdb=" O GLN H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 223 removed outlier: 4.339A pdb=" N GLN H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN H 201 " --> pdb=" O ILE H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.811A pdb=" N ILE H 236 " --> pdb=" O ALA H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 Processing helix chain 'I' and resid 82 through 102 removed outlier: 3.620A pdb=" N LYS I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 4.608A pdb=" N ASP I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY I 119 " --> pdb=" O ILE I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 4.681A pdb=" N ARG I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 154 removed outlier: 3.871A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY I 154 " --> pdb=" O TRP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.627A pdb=" N PHE I 188 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 194 removed outlier: 3.612A pdb=" N ASP I 194 " --> pdb=" O SER I 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 191 through 194' Processing helix chain 'I' and resid 197 through 209 removed outlier: 3.538A pdb=" N LEU I 207 " --> pdb=" O HIS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 232 through 246 removed outlier: 3.825A pdb=" N LEU I 238 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 281 Processing helix chain 'I' and resid 328 through 333 removed outlier: 3.605A pdb=" N CYS I 332 " --> pdb=" O SER I 328 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 333 " --> pdb=" O LEU I 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 333' Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 362 through 368 removed outlier: 3.673A pdb=" N ASN I 368 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 377 removed outlier: 3.590A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 400 Processing helix chain 'I' and resid 411 through 427 removed outlier: 3.727A pdb=" N PHE I 427 " --> pdb=" O ARG I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 430 No H-bonds generated for 'chain 'I' and resid 428 through 430' Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.637A pdb=" N GLU I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.519A pdb=" N SER I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP I 461 " --> pdb=" O GLN I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 483 Proline residue: I 472 - end of helix removed outlier: 4.927A pdb=" N ASP I 476 " --> pdb=" O PRO I 472 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 510 removed outlier: 3.906A pdb=" N MET I 510 " --> pdb=" O LEU I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 514 Processing helix chain 'I' and resid 525 through 551 removed outlier: 3.750A pdb=" N ASN I 531 " --> pdb=" O GLY I 527 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER I 532 " --> pdb=" O GLY I 528 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 569 removed outlier: 3.963A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS I 567 " --> pdb=" O ASP I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 575 Processing helix chain 'I' and resid 584 through 593 removed outlier: 3.578A pdb=" N LEU I 593 " --> pdb=" O TYR I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 625 removed outlier: 3.708A pdb=" N LEU I 600 " --> pdb=" O ASP I 596 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS I 619 " --> pdb=" O THR I 615 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 622 " --> pdb=" O LYS I 618 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL I 623 " --> pdb=" O LYS I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 652 removed outlier: 3.961A pdb=" N TYR I 637 " --> pdb=" O SER I 633 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 672 removed outlier: 4.219A pdb=" N LEU I 668 " --> pdb=" O ASP I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 697 Processing helix chain 'I' and resid 719 through 727 removed outlier: 3.558A pdb=" N GLY I 727 " --> pdb=" O LEU I 723 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 740 removed outlier: 3.545A pdb=" N HIS I 740 " --> pdb=" O ARG I 736 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 55 through 76 removed outlier: 3.610A pdb=" N SER K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 149 removed outlier: 3.975A pdb=" N GLN K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 188 Processing helix chain 'K' and resid 211 through 226 removed outlier: 3.514A pdb=" N MET K 215 " --> pdb=" O THR K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 Processing helix chain 'L' and resid 27 through 37 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 88 through 104 Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.806A pdb=" N GLU L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 removed outlier: 3.591A pdb=" N ILE L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 227 Processing helix chain 'L' and resid 257 through 269 removed outlier: 3.627A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.736A pdb=" N LEU L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 302 removed outlier: 3.543A pdb=" N THR L 302 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.697A pdb=" N VAL L 331 " --> pdb=" O TYR L 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 37 Processing helix chain 'M' and resid 74 through 85 removed outlier: 3.934A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.844A pdb=" N LEU M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.875A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 removed outlier: 3.706A pdb=" N THR M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.615A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 36 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 62 through 78 removed outlier: 4.184A pdb=" N ALA N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 3.770A pdb=" N LEU N 112 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'O' and resid 17 through 27 removed outlier: 3.681A pdb=" N GLN O 27 " --> pdb=" O ARG O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 109 Processing helix chain 'O' and resid 160 through 169 removed outlier: 3.961A pdb=" N ILE O 164 " --> pdb=" O PRO O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 200 Processing helix chain 'O' and resid 261 through 278 removed outlier: 3.969A pdb=" N GLU O 265 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 288 removed outlier: 3.568A pdb=" N VAL O 283 " --> pdb=" O PRO O 279 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE O 284 " --> pdb=" O LEU O 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 75 Processing helix chain 'P' and resid 147 through 161 removed outlier: 3.746A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 191 removed outlier: 3.611A pdb=" N HIS P 186 " --> pdb=" O ARG P 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU P 189 " --> pdb=" O LYS P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 250 removed outlier: 3.919A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 271 through 283 Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.820A pdb=" N ARG Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN Q 98 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 124 removed outlier: 3.919A pdb=" N ILE Q 106 " --> pdb=" O GLU Q 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 197 removed outlier: 3.881A pdb=" N GLU Q 191 " --> pdb=" O ALA Q 187 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU Q 193 " --> pdb=" O GLU Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 220 Processing helix chain 'Q' and resid 223 through 232 removed outlier: 3.882A pdb=" N GLU Q 227 " --> pdb=" O THR Q 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 248 removed outlier: 5.469A pdb=" N ASP Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE Q 244 " --> pdb=" O LYS Q 240 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 268 removed outlier: 3.738A pdb=" N LYS Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER Q 268 " --> pdb=" O LYS Q 264 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 267 removed outlier: 4.256A pdb=" N GLU U 257 " --> pdb=" O ILE U 253 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS U 262 " --> pdb=" O PHE U 258 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 369 removed outlier: 4.197A pdb=" N GLN U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG U 319 " --> pdb=" O LYS U 315 " (cutoff:3.500A) Proline residue: U 332 - end of helix removed outlier: 4.169A pdb=" N GLU U 346 " --> pdb=" O ASP U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 375 removed outlier: 4.061A pdb=" N GLU U 375 " --> pdb=" O VAL U 371 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 385 No H-bonds generated for 'chain 'U' and resid 383 through 385' Processing helix chain 'U' and resid 386 through 399 removed outlier: 4.506A pdb=" N THR U 396 " --> pdb=" O PHE U 392 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU U 397 " --> pdb=" O LYS U 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 415 Processing helix chain 'R' and resid 85 through 105 removed outlier: 4.236A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU R 99 " --> pdb=" O LYS R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 114 removed outlier: 3.666A pdb=" N GLU R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.847A pdb=" N GLU R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 4.337A pdb=" N LYS R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU R 142 " --> pdb=" O LYS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 177 removed outlier: 4.024A pdb=" N ILE R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN R 177 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 472 removed outlier: 4.341A pdb=" N HIS T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS T 472 " --> pdb=" O SER T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 506 removed outlier: 4.158A pdb=" N MET T 482 " --> pdb=" O LYS T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.657A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.776A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 removed outlier: 3.942A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 Processing helix chain 'W' and resid 38 through 65 removed outlier: 3.743A pdb=" N LEU W 42 " --> pdb=" O SER W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 87 removed outlier: 3.630A pdb=" N VAL W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 37 removed outlier: 4.163A pdb=" N LEU S 36 " --> pdb=" O GLU S 32 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 72 removed outlier: 3.818A pdb=" N GLU S 59 " --> pdb=" O PHE S 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN S 60 " --> pdb=" O ARG S 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 86 removed outlier: 3.687A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 120 Processing helix chain 'X' and resid 4 through 15 removed outlier: 3.512A pdb=" N VAL X 8 " --> pdb=" O ARG X 4 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS X 15 " --> pdb=" O LEU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 54 removed outlier: 3.564A pdb=" N VAL X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU X 33 " --> pdb=" O GLN X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 74 removed outlier: 3.691A pdb=" N VAL X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Proline residue: X 68 - end of helix removed outlier: 3.563A pdb=" N LEU X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 250 through 251 Processing sheet with id=AA2, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.079A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.079A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU L 240 " --> pdb=" O VAL L 305 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL L 307 " --> pdb=" O GLU L 238 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU L 238 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N LEU N 294 " --> pdb=" O GLU N 272 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N GLU N 272 " --> pdb=" O LEU N 294 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N LYS N 296 " --> pdb=" O LYS N 270 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N LYS N 270 " --> pdb=" O LYS N 296 " (cutoff:3.500A) removed outlier: 10.061A pdb=" N SER N 298 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N GLN N 268 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE N 266 " --> pdb=" O PRO N 300 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU N 264 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N PHE N 334 " --> pdb=" O PHE N 266 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN N 268 " --> pdb=" O PHE N 334 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE N 336 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS N 270 " --> pdb=" O ILE N 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'M' and resid 128 through 130 removed outlier: 6.477A pdb=" N ILE M 66 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU M 100 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE M 68 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR M 102 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL M 70 " --> pdb=" O THR M 102 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N LEU M 65 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR M 17 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 120 through 126 removed outlier: 4.687A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA N 161 " --> pdb=" O PHE N 86 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL N 85 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU N 193 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN N 87 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET N 191 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER N 89 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL N 189 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 117 removed outlier: 3.773A pdb=" N VAL O 122 " --> pdb=" O LEU O 142 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR O 128 " --> pdb=" O ASP O 136 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE O 130 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU O 134 " --> pdb=" O PHE O 130 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS O 152 " --> pdb=" O ASP O 141 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL O 143 " --> pdb=" O ILE O 150 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE O 150 " --> pdb=" O VAL O 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 217 through 224 removed outlier: 3.883A pdb=" N LEU O 224 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE O 231 " --> pdb=" O LEU O 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.139A pdb=" N SER P 108 " --> pdb=" O ARG P 79 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS P 81 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG P 106 " --> pdb=" O HIS P 81 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS P 83 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG P 104 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR P 85 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU P 102 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP P 87 " --> pdb=" O LYS P 100 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS P 100 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR P 115 " --> pdb=" O MET P 142 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET P 142 " --> pdb=" O THR P 115 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN P 117 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE P 140 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU P 119 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU P 138 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA P 134 " --> pdb=" O LEU P 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 195 through 196 removed outlier: 3.620A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU P 217 " --> pdb=" O LYS P 241 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS P 241 " --> pdb=" O GLU P 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'T' and resid 550 through 552 Processing sheet with id=AB6, first strand: chain 'S' and resid 76 through 77 1569 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4252 1.31 - 1.43: 7236 1.43 - 1.56: 15661 1.56 - 1.68: 162 1.68 - 1.81: 216 Bond restraints: 27527 Sorted by residual: bond pdb=" CA LYS L 70 " pdb=" C LYS L 70 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.24e-02 6.50e+03 2.03e+01 bond pdb=" C TRP L 72 " pdb=" O TRP L 72 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.23e-02 6.61e+03 2.02e+01 bond pdb=" C GLN L 71 " pdb=" O GLN L 71 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.21e-02 6.83e+03 1.64e+01 bond pdb=" CA GLN L 71 " pdb=" C GLN L 71 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C1' DG J 15 " pdb=" N9 DG J 15 " ideal model delta sigma weight residual 1.460 1.389 0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 27522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 37008 1.91 - 3.82: 397 3.82 - 5.73: 56 5.73 - 7.63: 12 7.63 - 9.54: 1 Bond angle restraints: 37474 Sorted by residual: angle pdb=" O3' DA i 17 " pdb=" C3' DA i 17 " pdb=" C2' DA i 17 " ideal model delta sigma weight residual 111.50 101.96 9.54 1.50e+00 4.44e-01 4.05e+01 angle pdb=" N GLU N 128 " pdb=" CA GLU N 128 " pdb=" C GLU N 128 " ideal model delta sigma weight residual 113.56 106.25 7.31 1.39e+00 5.18e-01 2.77e+01 angle pdb=" CA HIS L 69 " pdb=" C HIS L 69 " pdb=" N LYS L 70 " ideal model delta sigma weight residual 116.21 122.22 -6.01 1.29e+00 6.01e-01 2.17e+01 angle pdb=" O HIS L 69 " pdb=" C HIS L 69 " pdb=" N LYS L 70 " ideal model delta sigma weight residual 122.41 116.55 5.86 1.34e+00 5.57e-01 1.91e+01 angle pdb=" N LYS L 70 " pdb=" CA LYS L 70 " pdb=" C LYS L 70 " ideal model delta sigma weight residual 109.24 102.78 6.46 1.51e+00 4.39e-01 1.83e+01 ... (remaining 37469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14757 17.90 - 35.80: 1265 35.80 - 53.70: 486 53.70 - 71.60: 118 71.60 - 89.50: 28 Dihedral angle restraints: 16654 sinusoidal: 7403 harmonic: 9251 Sorted by residual: dihedral pdb=" CA GLN H 122 " pdb=" C GLN H 122 " pdb=" N SER H 123 " pdb=" CA SER H 123 " ideal model delta harmonic sigma weight residual -180.00 -147.51 -32.49 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA CYS P 111 " pdb=" C CYS P 111 " pdb=" N HIS P 112 " pdb=" CA HIS P 112 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER H 124 " pdb=" C SER H 124 " pdb=" N VAL H 125 " pdb=" CA VAL H 125 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 16651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3942 0.064 - 0.129: 347 0.129 - 0.193: 9 0.193 - 0.258: 0 0.258 - 0.322: 2 Chirality restraints: 4300 Sorted by residual: chirality pdb=" C3' DA i 17 " pdb=" C4' DA i 17 " pdb=" O3' DA i 17 " pdb=" C2' DA i 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.98 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE K 82 " pdb=" CA ILE K 82 " pdb=" CG1 ILE K 82 " pdb=" CG2 ILE K 82 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' DT J 3 " pdb=" C4' DT J 3 " pdb=" O3' DT J 3 " pdb=" C2' DT J 3 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 4297 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS P 111 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C CYS P 111 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS P 111 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS P 112 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA i 16 " -0.025 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 DA i 16 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA i 16 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA i 16 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA i 16 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA i 16 " -0.011 2.00e-02 2.50e+03 pdb=" N6 DA i 16 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DA i 16 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA i 16 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DA i 16 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA i 16 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT i 21 " -0.024 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" N1 DT i 21 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DT i 21 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT i 21 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DT i 21 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT i 21 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT i 21 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DT i 21 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT i 21 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT i 21 " 0.015 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 22 2.30 - 2.95: 11199 2.95 - 3.60: 39754 3.60 - 4.25: 59170 4.25 - 4.90: 99120 Nonbonded interactions: 209265 Sorted by model distance: nonbonded pdb=" N3 DG J 5 " pdb=" N2 DG i -3 " model vdw 1.653 3.200 nonbonded pdb=" C2' DA i 20 " pdb=" C7 DT i 21 " model vdw 1.767 3.860 nonbonded pdb=" N1 DG J 5 " pdb=" N1 DG i -3 " model vdw 1.772 3.200 nonbonded pdb=" C2 DG J 5 " pdb=" N2 DG i -3 " model vdw 1.832 3.340 nonbonded pdb=" C2 DG J 5 " pdb=" C2 DG i -3 " model vdw 1.919 3.480 ... (remaining 209260 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.530 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.003 0.071 27527 Z= 0.165 Angle : 0.510 9.542 37474 Z= 0.302 Chirality : 0.037 0.322 4300 Planarity : 0.003 0.044 4432 Dihedral : 16.184 89.496 10582 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.82 % Allowed : 8.35 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3064 helix: 0.27 (0.11), residues: 1899 sheet: -0.32 (0.29), residues: 307 loop : -1.96 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 56 TYR 0.012 0.001 TYR O 239 PHE 0.013 0.001 PHE I 482 TRP 0.024 0.001 TRP L 72 HIS 0.003 0.000 HIS P 112 Details of bonding type rmsd covalent geometry : bond 0.00315 (27527) covalent geometry : angle 0.51031 (37474) hydrogen bonds : bond 0.12180 ( 1642) hydrogen bonds : angle 4.81748 ( 4789) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 1.070 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: Q 93 MET cc_start: 0.8997 (ttp) cc_final: 0.8670 (tmt) REVERT: U 289 PHE cc_start: 0.8464 (m-10) cc_final: 0.8048 (m-80) REVERT: U 383 ASP cc_start: 0.7612 (p0) cc_final: 0.7197 (p0) REVERT: U 406 ASN cc_start: 0.8736 (m-40) cc_final: 0.8368 (m-40) REVERT: R 86 PHE cc_start: 0.4342 (m-80) cc_final: 0.4071 (m-10) REVERT: R 87 MET cc_start: 0.7825 (mmm) cc_final: 0.7462 (mmp) REVERT: T 478 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8747 (mmmm) REVERT: S 13 PHE cc_start: 0.8452 (t80) cc_final: 0.8148 (t80) REVERT: S 57 GLN cc_start: 0.7745 (tp40) cc_final: 0.7141 (tm-30) REVERT: X 5 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7589 (mmtt) REVERT: X 6 GLU cc_start: 0.6962 (tp30) cc_final: 0.6643 (tp30) REVERT: X 41 GLU cc_start: 0.8466 (tp30) cc_final: 0.7962 (tm-30) REVERT: X 49 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8872 (tm-30) REVERT: X 69 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8745 (tm-30) outliers start: 23 outliers final: 10 residues processed: 350 average time/residue: 0.8680 time to fit residues: 339.5839 Evaluate side-chains 239 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 229 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain Q residue 108 TYR Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain X residue 59 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 182 GLN H 191 ASN H 203 GLN I 97 ASN I 193 GLN I 349 GLN I 352 GLN I 374 HIS I 394 GLN I 608 HIS L 51 GLN L 201 GLN M 156 HIS N 78 GLN N 80 GLN N 177 GLN N 185 HIS O 198 GLN O 267 GLN P 112 HIS Q 111 ASN Q 177 GLN Q 181 ASN Q 202 GLN Q 204 ASN U 406 ASN R 111 GLN R 130 HIS R 147 ASN T 555 ASN S 16 GLN X 29 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.082151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048574 restraints weight = 89382.620| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.04 r_work: 0.2746 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27527 Z= 0.265 Angle : 0.657 11.845 37474 Z= 0.348 Chirality : 0.043 0.202 4300 Planarity : 0.004 0.054 4432 Dihedral : 16.527 126.189 4233 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.45 % Allowed : 14.43 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3064 helix: 1.26 (0.12), residues: 1931 sheet: 0.03 (0.30), residues: 296 loop : -1.44 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 48 TYR 0.018 0.002 TYR P 196 PHE 0.028 0.002 PHE I 583 TRP 0.015 0.002 TRP I 718 HIS 0.015 0.001 HIS P 112 Details of bonding type rmsd covalent geometry : bond 0.00636 (27527) covalent geometry : angle 0.65691 (37474) hydrogen bonds : bond 0.06904 ( 1642) hydrogen bonds : angle 3.90102 ( 4789) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 249 time to evaluate : 0.811 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: H 40 MET cc_start: 0.8939 (mmm) cc_final: 0.8610 (mmt) REVERT: H 60 MET cc_start: 0.9286 (tpp) cc_final: 0.8253 (mpp) REVERT: I 135 PRO cc_start: 0.7949 (Cg_exo) cc_final: 0.7733 (Cg_endo) REVERT: I 514 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.5696 (mpp) REVERT: K 26 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8269 (mtt90) REVERT: N 18 MET cc_start: 0.9157 (mmm) cc_final: 0.8944 (tpt) REVERT: O 25 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: O 167 LYS cc_start: 0.9407 (tmmm) cc_final: 0.9185 (tmtm) REVERT: O 191 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8860 (tttm) REVERT: Q 93 MET cc_start: 0.9352 (ttp) cc_final: 0.8876 (tmm) REVERT: Q 172 MET cc_start: 0.8615 (ttm) cc_final: 0.8414 (ttp) REVERT: U 309 MET cc_start: 0.8251 (ttp) cc_final: 0.8020 (ttp) REVERT: U 406 ASN cc_start: 0.8789 (m110) cc_final: 0.8443 (m-40) REVERT: R 86 PHE cc_start: 0.5200 (m-80) cc_final: 0.4866 (m-10) REVERT: R 87 MET cc_start: 0.8281 (mmm) cc_final: 0.8027 (mmp) REVERT: T 476 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7321 (mt-10) REVERT: T 480 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8100 (mm) REVERT: W 1 MET cc_start: 0.7426 (pmm) cc_final: 0.7072 (pmm) REVERT: W 68 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8423 (ptm-80) REVERT: S 37 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8605 (p0) REVERT: S 83 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8867 (mtmm) REVERT: X 41 GLU cc_start: 0.7939 (tp30) cc_final: 0.7550 (tm-30) REVERT: X 49 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8397 (tm-30) REVERT: X 64 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: X 69 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8461 (tp-100) outliers start: 69 outliers final: 30 residues processed: 293 average time/residue: 0.8672 time to fit residues: 284.8718 Evaluate side-chains 255 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 410 HIS Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 191 LYS Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain U residue 268 ARG Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 480 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 204 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 220 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 201 ASN H 214 HIS M 144 GLN P 112 HIS R 130 HIS T 545 GLN S 24 HIS X 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.083742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050850 restraints weight = 88212.920| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.97 r_work: 0.2814 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27527 Z= 0.128 Angle : 0.553 9.735 37474 Z= 0.293 Chirality : 0.038 0.200 4300 Planarity : 0.004 0.052 4432 Dihedral : 16.257 80.378 4224 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.85 % Allowed : 16.60 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.28 (0.15), residues: 3064 helix: 1.79 (0.12), residues: 1930 sheet: 0.29 (0.30), residues: 296 loop : -1.17 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 48 TYR 0.013 0.001 TYR O 239 PHE 0.028 0.001 PHE O 287 TRP 0.012 0.001 TRP I 718 HIS 0.016 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00266 (27527) covalent geometry : angle 0.55312 (37474) hydrogen bonds : bond 0.05221 ( 1642) hydrogen bonds : angle 3.58254 ( 4789) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.092 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: H 60 MET cc_start: 0.9234 (tpp) cc_final: 0.8091 (mpp) REVERT: H 123 SER cc_start: 0.5064 (OUTLIER) cc_final: 0.4666 (m) REVERT: H 189 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7448 (tmm) REVERT: I 128 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8906 (ptm160) REVERT: I 135 PRO cc_start: 0.7460 (Cg_exo) cc_final: 0.6927 (Cg_endo) REVERT: I 171 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: I 514 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.5594 (mpp) REVERT: M 86 ARG cc_start: 0.9069 (mtm110) cc_final: 0.8781 (mtm180) REVERT: O 25 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: O 106 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8384 (mm110) REVERT: O 167 LYS cc_start: 0.9403 (tmmm) cc_final: 0.9160 (tmtm) REVERT: Q 93 MET cc_start: 0.9345 (ttp) cc_final: 0.8838 (tmt) REVERT: Q 134 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7847 (mt) REVERT: U 406 ASN cc_start: 0.8711 (m110) cc_final: 0.8349 (m-40) REVERT: R 86 PHE cc_start: 0.5251 (m-80) cc_final: 0.4887 (m-10) REVERT: R 87 MET cc_start: 0.8275 (mmm) cc_final: 0.7981 (mmp) REVERT: T 476 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7436 (mt-10) REVERT: W 1 MET cc_start: 0.7330 (pmm) cc_final: 0.6774 (pmm) REVERT: X 6 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6637 (tm-30) REVERT: X 33 GLU cc_start: 0.8076 (tp30) cc_final: 0.7796 (tp30) REVERT: X 41 GLU cc_start: 0.7919 (tp30) cc_final: 0.7509 (tm-30) REVERT: X 48 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7788 (mtm110) REVERT: X 49 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8397 (tm-30) REVERT: X 69 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8443 (tp-100) outliers start: 52 outliers final: 15 residues processed: 283 average time/residue: 0.8199 time to fit residues: 260.4820 Evaluate side-chains 241 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 218 LEU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain U residue 407 ILE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 227 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 256 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 ASN I 397 GLN P 112 HIS Q 142 ASN R 130 HIS S 11 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049227 restraints weight = 87673.488| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.01 r_work: 0.2766 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27527 Z= 0.174 Angle : 0.587 10.076 37474 Z= 0.309 Chirality : 0.039 0.189 4300 Planarity : 0.004 0.052 4432 Dihedral : 16.236 80.395 4219 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.28 % Allowed : 17.13 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.49 (0.15), residues: 3064 helix: 1.93 (0.12), residues: 1940 sheet: 0.33 (0.30), residues: 296 loop : -1.05 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 304 TYR 0.013 0.001 TYR I 565 PHE 0.023 0.001 PHE O 287 TRP 0.013 0.001 TRP I 718 HIS 0.018 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00406 (27527) covalent geometry : angle 0.58672 (37474) hydrogen bonds : bond 0.05963 ( 1642) hydrogen bonds : angle 3.64923 ( 4789) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 1.035 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: H 40 MET cc_start: 0.8876 (mmm) cc_final: 0.8539 (mmt) REVERT: I 128 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8924 (ptm160) REVERT: I 135 PRO cc_start: 0.7536 (Cg_exo) cc_final: 0.7066 (Cg_endo) REVERT: I 171 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7848 (mtt) REVERT: I 177 ARG cc_start: 0.8112 (mpp80) cc_final: 0.7738 (mtm180) REVERT: I 514 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.5636 (mpp) REVERT: M 86 ARG cc_start: 0.9054 (mtm110) cc_final: 0.8788 (mtm180) REVERT: N 18 MET cc_start: 0.9090 (tpt) cc_final: 0.8835 (mmm) REVERT: O 25 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: O 106 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8372 (mm110) REVERT: P 137 ASP cc_start: 0.8931 (t0) cc_final: 0.8705 (t0) REVERT: P 244 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7686 (tm-30) REVERT: Q 87 MET cc_start: 0.8924 (tpt) cc_final: 0.8640 (tpp) REVERT: Q 88 MET cc_start: 0.8926 (mtp) cc_final: 0.8708 (mtm) REVERT: Q 93 MET cc_start: 0.9365 (ttp) cc_final: 0.8787 (tmt) REVERT: Q 172 MET cc_start: 0.8584 (ttm) cc_final: 0.8351 (ttp) REVERT: Q 203 ILE cc_start: 0.7181 (mm) cc_final: 0.6544 (tp) REVERT: U 406 ASN cc_start: 0.8730 (m110) cc_final: 0.8349 (m-40) REVERT: R 86 PHE cc_start: 0.5284 (m-80) cc_final: 0.4927 (m-10) REVERT: R 87 MET cc_start: 0.8276 (mmm) cc_final: 0.8022 (mmp) REVERT: T 476 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7417 (mt-10) REVERT: W 1 MET cc_start: 0.7426 (pmm) cc_final: 0.7155 (pmm) REVERT: S 37 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8628 (p0) REVERT: S 83 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8835 (mtmm) REVERT: X 5 LYS cc_start: 0.7459 (mmmm) cc_final: 0.6153 (mmtt) REVERT: X 6 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6657 (tm-30) REVERT: X 29 GLN cc_start: 0.9270 (tp40) cc_final: 0.8678 (mp10) REVERT: X 33 GLU cc_start: 0.8217 (tp30) cc_final: 0.7798 (tp30) REVERT: X 41 GLU cc_start: 0.7926 (tp30) cc_final: 0.7497 (tm-30) REVERT: X 49 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8385 (tm-30) REVERT: X 64 GLU cc_start: 0.8585 (mp0) cc_final: 0.8145 (mp0) REVERT: X 69 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8421 (tp-100) outliers start: 64 outliers final: 23 residues processed: 290 average time/residue: 0.7750 time to fit residues: 253.7541 Evaluate side-chains 251 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain X residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 276 optimal weight: 0.1980 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 ASN I 638 GLN P 59 GLN P 112 HIS R 130 HIS S 11 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.083485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050411 restraints weight = 87426.505| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.99 r_work: 0.2804 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27527 Z= 0.130 Angle : 0.562 9.680 37474 Z= 0.295 Chirality : 0.038 0.192 4300 Planarity : 0.004 0.051 4432 Dihedral : 16.165 81.140 4218 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.67 % Allowed : 18.45 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.75 (0.16), residues: 3064 helix: 2.12 (0.12), residues: 1939 sheet: 0.41 (0.30), residues: 301 loop : -0.89 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG X 48 TYR 0.021 0.001 TYR S 25 PHE 0.026 0.001 PHE O 287 TRP 0.012 0.001 TRP I 718 HIS 0.017 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00282 (27527) covalent geometry : angle 0.56178 (37474) hydrogen bonds : bond 0.05174 ( 1642) hydrogen bonds : angle 3.51022 ( 4789) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.8881 (mmm) cc_final: 0.8528 (mmt) REVERT: H 229 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: I 128 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8959 (ptm160) REVERT: I 177 ARG cc_start: 0.8197 (mpp80) cc_final: 0.7805 (mtm180) REVERT: I 514 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.5609 (mpp) REVERT: K 26 ARG cc_start: 0.8638 (mtt90) cc_final: 0.8338 (mtt90) REVERT: M 86 ARG cc_start: 0.9048 (mtm110) cc_final: 0.8721 (mtm180) REVERT: N 18 MET cc_start: 0.9062 (tpt) cc_final: 0.8793 (mmm) REVERT: O 25 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: O 106 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8303 (mm110) REVERT: P 137 ASP cc_start: 0.8943 (t0) cc_final: 0.8653 (t0) REVERT: Q 87 MET cc_start: 0.9013 (tpt) cc_final: 0.8688 (tpp) REVERT: Q 93 MET cc_start: 0.9370 (ttp) cc_final: 0.8804 (tmt) REVERT: Q 203 ILE cc_start: 0.7295 (mm) cc_final: 0.6657 (tp) REVERT: U 309 MET cc_start: 0.8140 (ttp) cc_final: 0.7911 (ttm) REVERT: U 374 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8483 (pp30) REVERT: U 406 ASN cc_start: 0.8724 (m110) cc_final: 0.8373 (m-40) REVERT: T 476 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7554 (mt-10) REVERT: W 1 MET cc_start: 0.7387 (pmm) cc_final: 0.6967 (pmm) REVERT: S 67 MET cc_start: 0.8509 (ttp) cc_final: 0.8247 (ttm) REVERT: X 5 LYS cc_start: 0.7419 (mmmm) cc_final: 0.6893 (mmtt) REVERT: X 6 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6360 (tm-30) REVERT: X 33 GLU cc_start: 0.8281 (tp30) cc_final: 0.7749 (tp30) REVERT: X 41 GLU cc_start: 0.7896 (tp30) cc_final: 0.7441 (tm-30) REVERT: X 48 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7603 (mtm110) REVERT: X 49 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8250 (tm-30) REVERT: X 64 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: X 69 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8388 (tp-100) outliers start: 47 outliers final: 17 residues processed: 279 average time/residue: 0.8267 time to fit residues: 259.6409 Evaluate side-chains 241 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 218 LEU Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 374 GLN Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 131 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 222 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 296 optimal weight: 0.3980 chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 177 GLN P 112 HIS R 130 HIS T 545 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.083273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050026 restraints weight = 88726.209| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.05 r_work: 0.2788 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27527 Z= 0.138 Angle : 0.586 11.399 37474 Z= 0.304 Chirality : 0.038 0.186 4300 Planarity : 0.004 0.051 4432 Dihedral : 16.125 81.051 4218 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.10 % Allowed : 18.84 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.16), residues: 3064 helix: 2.21 (0.12), residues: 1942 sheet: 0.47 (0.30), residues: 301 loop : -0.80 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 48 TYR 0.021 0.001 TYR I 72 PHE 0.025 0.001 PHE O 287 TRP 0.012 0.001 TRP I 718 HIS 0.018 0.001 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00307 (27527) covalent geometry : angle 0.58550 (37474) hydrogen bonds : bond 0.05287 ( 1642) hydrogen bonds : angle 3.48844 ( 4789) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 1.246 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: H 40 MET cc_start: 0.8897 (mmm) cc_final: 0.8696 (mmt) REVERT: H 119 ILE cc_start: 0.9156 (mp) cc_final: 0.8732 (tp) REVERT: H 229 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: I 128 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8934 (ptm160) REVERT: I 177 ARG cc_start: 0.8206 (mpp80) cc_final: 0.7920 (mpp80) REVERT: I 514 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.5637 (mpp) REVERT: K 26 ARG cc_start: 0.8688 (mtt90) cc_final: 0.8469 (mtt90) REVERT: M 86 ARG cc_start: 0.9056 (mtm110) cc_final: 0.8747 (mtm180) REVERT: N 18 MET cc_start: 0.9049 (tpt) cc_final: 0.8752 (mmm) REVERT: O 25 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: O 106 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8351 (mm110) REVERT: P 112 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8010 (t-170) REVERT: P 137 ASP cc_start: 0.9013 (t0) cc_final: 0.8734 (t0) REVERT: P 247 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8310 (tt) REVERT: Q 93 MET cc_start: 0.9362 (ttp) cc_final: 0.8772 (tmt) REVERT: Q 203 ILE cc_start: 0.7380 (mm) cc_final: 0.6721 (tp) REVERT: U 281 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.5296 (p90) REVERT: U 309 MET cc_start: 0.8188 (ttp) cc_final: 0.7896 (ttm) REVERT: U 406 ASN cc_start: 0.8745 (m110) cc_final: 0.8396 (m-40) REVERT: R 104 MET cc_start: 0.8261 (tpt) cc_final: 0.7321 (ptt) REVERT: T 476 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7614 (mt-10) REVERT: W 1 MET cc_start: 0.7378 (pmm) cc_final: 0.7070 (pmm) REVERT: S 11 GLN cc_start: 0.8972 (mm110) cc_final: 0.8480 (tm-30) REVERT: S 38 LYS cc_start: 0.8581 (tptp) cc_final: 0.8171 (tptp) REVERT: S 67 MET cc_start: 0.8496 (ttp) cc_final: 0.8249 (ttm) REVERT: X 6 GLU cc_start: 0.6698 (tm-30) cc_final: 0.6430 (tm-30) REVERT: X 33 GLU cc_start: 0.8407 (tp30) cc_final: 0.7914 (tp30) REVERT: X 41 GLU cc_start: 0.7909 (tp30) cc_final: 0.7434 (tm-30) REVERT: X 49 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8282 (tm-30) REVERT: X 64 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: X 69 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8413 (tp-100) outliers start: 59 outliers final: 25 residues processed: 285 average time/residue: 0.7821 time to fit residues: 252.2424 Evaluate side-chains 251 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 250 VAL Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 131 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 515 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 26 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 HIS P 112 HIS ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.081425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047895 restraints weight = 88216.990| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.03 r_work: 0.2724 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 27527 Z= 0.232 Angle : 0.652 10.376 37474 Z= 0.342 Chirality : 0.042 0.203 4300 Planarity : 0.004 0.055 4432 Dihedral : 16.264 80.864 4218 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.74 % Allowed : 20.26 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.69 (0.15), residues: 3064 helix: 2.06 (0.12), residues: 1930 sheet: 0.38 (0.30), residues: 297 loop : -0.86 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG X 48 TYR 0.020 0.002 TYR I 72 PHE 0.026 0.002 PHE I 583 TRP 0.015 0.001 TRP I 718 HIS 0.028 0.001 HIS P 112 Details of bonding type rmsd covalent geometry : bond 0.00557 (27527) covalent geometry : angle 0.65195 (37474) hydrogen bonds : bond 0.06695 ( 1642) hydrogen bonds : angle 3.75412 ( 4789) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 119 ILE cc_start: 0.9230 (mp) cc_final: 0.8870 (tp) REVERT: H 229 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: I 128 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.9026 (ptp-170) REVERT: I 177 ARG cc_start: 0.8228 (mpp80) cc_final: 0.7952 (mpp80) REVERT: I 510 MET cc_start: 0.8690 (mmp) cc_final: 0.7889 (mmp) REVERT: I 514 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.5666 (mpp) REVERT: N 18 MET cc_start: 0.9171 (tpt) cc_final: 0.8958 (tpt) REVERT: O 25 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: P 137 ASP cc_start: 0.9085 (t0) cc_final: 0.8822 (t0) REVERT: Q 87 MET cc_start: 0.8899 (tpt) cc_final: 0.8562 (tpp) REVERT: Q 93 MET cc_start: 0.9365 (ttp) cc_final: 0.8759 (tmm) REVERT: U 281 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5317 (p90) REVERT: U 406 ASN cc_start: 0.8782 (m110) cc_final: 0.8415 (m-40) REVERT: R 104 MET cc_start: 0.8346 (tpt) cc_final: 0.8024 (mmm) REVERT: T 476 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7601 (mt-10) REVERT: S 11 GLN cc_start: 0.9009 (mm110) cc_final: 0.8512 (tm-30) REVERT: S 38 LYS cc_start: 0.8625 (tptp) cc_final: 0.8276 (tptm) REVERT: S 67 MET cc_start: 0.8574 (ttp) cc_final: 0.8371 (ttm) REVERT: X 6 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7344 (tm-30) REVERT: X 33 GLU cc_start: 0.8456 (tp30) cc_final: 0.8063 (tp30) REVERT: X 41 GLU cc_start: 0.7838 (tp30) cc_final: 0.7415 (tm-30) REVERT: X 48 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7387 (mtm110) REVERT: X 49 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8293 (tm-30) REVERT: X 64 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: X 69 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8371 (tp-100) outliers start: 49 outliers final: 27 residues processed: 258 average time/residue: 0.7982 time to fit residues: 233.0475 Evaluate side-chains 243 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 434 SER Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 515 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 157 optimal weight: 0.9980 chunk 264 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.082795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049949 restraints weight = 87727.753| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.95 r_work: 0.2787 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27527 Z= 0.133 Angle : 0.614 13.459 37474 Z= 0.317 Chirality : 0.039 0.218 4300 Planarity : 0.004 0.052 4432 Dihedral : 16.150 82.145 4217 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.28 % Allowed : 21.15 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.16), residues: 3064 helix: 2.20 (0.12), residues: 1943 sheet: 0.41 (0.30), residues: 302 loop : -0.76 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 48 TYR 0.023 0.001 TYR I 72 PHE 0.026 0.001 PHE O 287 TRP 0.011 0.001 TRP I 718 HIS 0.013 0.001 HIS P 112 Details of bonding type rmsd covalent geometry : bond 0.00286 (27527) covalent geometry : angle 0.61375 (37474) hydrogen bonds : bond 0.05360 ( 1642) hydrogen bonds : angle 3.53761 ( 4789) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.8921 (mmm) cc_final: 0.8606 (mmt) REVERT: H 119 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8858 (tp) REVERT: H 229 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: I 128 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.9022 (ptp-170) REVERT: I 177 ARG cc_start: 0.8282 (mpp80) cc_final: 0.7985 (mpp80) REVERT: I 514 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.5630 (mpp) REVERT: M 86 ARG cc_start: 0.9041 (mtm110) cc_final: 0.8725 (mtm180) REVERT: N 18 MET cc_start: 0.9056 (tpt) cc_final: 0.8855 (tpt) REVERT: O 25 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: O 106 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8373 (mm110) REVERT: P 112 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8389 (t70) REVERT: P 137 ASP cc_start: 0.9053 (t0) cc_final: 0.8731 (t0) REVERT: Q 87 MET cc_start: 0.8952 (tpt) cc_final: 0.8622 (tpp) REVERT: Q 93 MET cc_start: 0.9346 (ttp) cc_final: 0.8748 (tmt) REVERT: U 309 MET cc_start: 0.8186 (ttp) cc_final: 0.7985 (ttm) REVERT: U 406 ASN cc_start: 0.8811 (m110) cc_final: 0.8456 (m-40) REVERT: R 104 MET cc_start: 0.8363 (tpt) cc_final: 0.7468 (ptt) REVERT: R 130 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7376 (m90) REVERT: T 476 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7658 (mt-10) REVERT: W 1 MET cc_start: 0.7171 (pmm) cc_final: 0.6801 (pmm) REVERT: S 6 GLU cc_start: 0.8360 (tp30) cc_final: 0.7751 (pp20) REVERT: S 11 GLN cc_start: 0.8996 (mm110) cc_final: 0.8516 (tm-30) REVERT: S 38 LYS cc_start: 0.8628 (tptp) cc_final: 0.8364 (tptp) REVERT: S 45 GLN cc_start: 0.8035 (pm20) cc_final: 0.7811 (pm20) REVERT: S 67 MET cc_start: 0.8497 (ttp) cc_final: 0.8271 (ttm) REVERT: X 6 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7290 (tm-30) REVERT: X 33 GLU cc_start: 0.8582 (tp30) cc_final: 0.7977 (tp30) REVERT: X 41 GLU cc_start: 0.7876 (tp30) cc_final: 0.7499 (tm-30) REVERT: X 49 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8311 (tm-30) REVERT: X 64 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: X 69 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8390 (tp-100) outliers start: 36 outliers final: 19 residues processed: 246 average time/residue: 0.8256 time to fit residues: 228.2482 Evaluate side-chains 239 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 130 HIS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 515 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 181 optimal weight: 0.2980 chunk 186 optimal weight: 0.0170 chunk 200 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS X 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.083319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050296 restraints weight = 88365.069| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.00 r_work: 0.2799 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27527 Z= 0.131 Angle : 0.620 12.086 37474 Z= 0.320 Chirality : 0.038 0.202 4300 Planarity : 0.004 0.060 4432 Dihedral : 16.046 81.947 4217 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.39 % Allowed : 21.01 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.99 (0.16), residues: 3064 helix: 2.25 (0.12), residues: 1942 sheet: 0.51 (0.30), residues: 302 loop : -0.66 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG X 48 TYR 0.025 0.001 TYR I 72 PHE 0.025 0.001 PHE O 287 TRP 0.011 0.001 TRP I 718 HIS 0.021 0.001 HIS P 112 Details of bonding type rmsd covalent geometry : bond 0.00283 (27527) covalent geometry : angle 0.61956 (37474) hydrogen bonds : bond 0.05178 ( 1642) hydrogen bonds : angle 3.49056 ( 4789) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.976 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: H 40 MET cc_start: 0.8885 (mmm) cc_final: 0.8579 (mmt) REVERT: H 119 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8941 (tp) REVERT: H 229 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: I 128 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.9036 (ptp-170) REVERT: I 177 ARG cc_start: 0.8282 (mpp80) cc_final: 0.7874 (mpp80) REVERT: I 514 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.5669 (mpp) REVERT: M 86 ARG cc_start: 0.9023 (mtm110) cc_final: 0.8699 (mtm180) REVERT: N 18 MET cc_start: 0.9034 (tpt) cc_final: 0.8710 (mmm) REVERT: O 25 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: P 137 ASP cc_start: 0.9041 (t0) cc_final: 0.8712 (t0) REVERT: Q 87 MET cc_start: 0.8986 (tpt) cc_final: 0.8649 (tpp) REVERT: Q 93 MET cc_start: 0.9350 (ttp) cc_final: 0.8758 (tmt) REVERT: U 281 PHE cc_start: 0.5859 (OUTLIER) cc_final: 0.5320 (p90) REVERT: U 309 MET cc_start: 0.8181 (ttp) cc_final: 0.7939 (ttm) REVERT: U 406 ASN cc_start: 0.8777 (m110) cc_final: 0.8426 (m-40) REVERT: R 104 MET cc_start: 0.8330 (tpt) cc_final: 0.7405 (ptt) REVERT: T 476 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7666 (mt-10) REVERT: W 1 MET cc_start: 0.7155 (pmm) cc_final: 0.6856 (pmm) REVERT: S 6 GLU cc_start: 0.8255 (tp30) cc_final: 0.7723 (pp20) REVERT: S 11 GLN cc_start: 0.9019 (mm110) cc_final: 0.8564 (tm-30) REVERT: S 12 ARG cc_start: 0.8918 (ptm160) cc_final: 0.8492 (ptm160) REVERT: S 15 TYR cc_start: 0.7813 (t80) cc_final: 0.7323 (t80) REVERT: S 38 LYS cc_start: 0.8636 (tptp) cc_final: 0.8373 (tptp) REVERT: S 67 MET cc_start: 0.8440 (ttp) cc_final: 0.8217 (ttm) REVERT: X 33 GLU cc_start: 0.8504 (tp30) cc_final: 0.8001 (tp30) REVERT: X 41 GLU cc_start: 0.7902 (tp30) cc_final: 0.7303 (tm-30) REVERT: X 45 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7677 (tpp80) REVERT: X 49 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8232 (tm-30) REVERT: X 59 ASP cc_start: 0.7538 (m-30) cc_final: 0.7264 (m-30) REVERT: X 64 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: X 69 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8414 (tp-100) REVERT: X 73 ASP cc_start: 0.8490 (t0) cc_final: 0.8283 (t0) outliers start: 39 outliers final: 21 residues processed: 251 average time/residue: 0.8494 time to fit residues: 239.9295 Evaluate side-chains 244 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 342 ASP Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 515 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 26 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 236 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS ** U 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.083255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.050349 restraints weight = 87618.326| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.02 r_work: 0.2801 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27527 Z= 0.133 Angle : 0.636 13.043 37474 Z= 0.328 Chirality : 0.038 0.231 4300 Planarity : 0.004 0.053 4432 Dihedral : 15.998 81.819 4217 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.21 % Allowed : 21.40 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.00 (0.16), residues: 3064 helix: 2.24 (0.12), residues: 1943 sheet: 0.56 (0.30), residues: 302 loop : -0.64 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG X 48 TYR 0.028 0.001 TYR S 15 PHE 0.025 0.001 PHE O 287 TRP 0.011 0.001 TRP I 718 HIS 0.011 0.001 HIS P 112 Details of bonding type rmsd covalent geometry : bond 0.00291 (27527) covalent geometry : angle 0.63603 (37474) hydrogen bonds : bond 0.05111 ( 1642) hydrogen bonds : angle 3.50693 ( 4789) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.8881 (mmm) cc_final: 0.8562 (mmt) REVERT: H 119 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9003 (tp) REVERT: H 229 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: I 128 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.9028 (ptp-170) REVERT: I 177 ARG cc_start: 0.8305 (mpp80) cc_final: 0.7900 (mpp80) REVERT: L 35 ARG cc_start: 0.8353 (tpm170) cc_final: 0.7889 (tpm170) REVERT: M 86 ARG cc_start: 0.9023 (mtm110) cc_final: 0.8781 (mtm180) REVERT: N 18 MET cc_start: 0.9007 (tpt) cc_final: 0.8684 (mmm) REVERT: N 128 GLU cc_start: 0.7691 (pm20) cc_final: 0.6849 (pm20) REVERT: O 25 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: P 112 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.8421 (t-170) REVERT: P 137 ASP cc_start: 0.9079 (t0) cc_final: 0.8774 (t0) REVERT: Q 87 MET cc_start: 0.9022 (tpt) cc_final: 0.8688 (tpp) REVERT: Q 93 MET cc_start: 0.9353 (ttp) cc_final: 0.8761 (tmt) REVERT: U 281 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.5340 (p90) REVERT: U 309 MET cc_start: 0.8190 (ttp) cc_final: 0.7965 (ttm) REVERT: U 406 ASN cc_start: 0.8813 (m110) cc_final: 0.8460 (m-40) REVERT: R 104 MET cc_start: 0.8375 (tpt) cc_final: 0.7417 (ptt) REVERT: T 476 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7713 (mt-10) REVERT: T 481 GLU cc_start: 0.8232 (pm20) cc_final: 0.7947 (pm20) REVERT: T 484 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8348 (pm20) REVERT: W 1 MET cc_start: 0.7086 (pmm) cc_final: 0.6773 (pmm) REVERT: S 6 GLU cc_start: 0.8281 (tp30) cc_final: 0.7758 (pp20) REVERT: S 11 GLN cc_start: 0.9042 (mm110) cc_final: 0.8590 (tm-30) REVERT: S 12 ARG cc_start: 0.8900 (ptm160) cc_final: 0.8537 (ptm160) REVERT: S 38 LYS cc_start: 0.8682 (tptp) cc_final: 0.8406 (tptp) REVERT: S 67 MET cc_start: 0.8451 (ttp) cc_final: 0.8225 (ttm) REVERT: X 33 GLU cc_start: 0.8515 (tp30) cc_final: 0.8001 (tp30) REVERT: X 49 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8343 (tm-30) REVERT: X 59 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: X 64 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: X 69 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8343 (tp-100) outliers start: 34 outliers final: 18 residues processed: 248 average time/residue: 0.8210 time to fit residues: 229.4442 Evaluate side-chains 241 residues out of total 2861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 281 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 112 HIS Q 136 ASN ** U 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.083322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050439 restraints weight = 86889.262| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.99 r_work: 0.2807 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27527 Z= 0.135 Angle : 0.641 12.578 37474 Z= 0.333 Chirality : 0.038 0.218 4300 Planarity : 0.004 0.057 4432 Dihedral : 15.952 81.691 4217 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.21 % Allowed : 21.44 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.99 (0.16), residues: 3064 helix: 2.22 (0.12), residues: 1945 sheet: 0.61 (0.31), residues: 302 loop : -0.63 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG S 18 TYR 0.028 0.001 TYR S 15 PHE 0.025 0.001 PHE O 287 TRP 0.012 0.001 TRP K 239 HIS 0.023 0.001 HIS P 112 Details of bonding type rmsd covalent geometry : bond 0.00297 (27527) covalent geometry : angle 0.64149 (37474) hydrogen bonds : bond 0.05083 ( 1642) hydrogen bonds : angle 3.52037 ( 4789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12202.62 seconds wall clock time: 207 minutes 22.54 seconds (12442.54 seconds total)