Starting phenix.real_space_refine on Tue Jun 17 21:32:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u0p_8479/06_2025/5u0p_8479.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u0p_8479/06_2025/5u0p_8479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u0p_8479/06_2025/5u0p_8479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u0p_8479/06_2025/5u0p_8479.map" model { file = "/net/cci-nas-00/data/ceres_data/5u0p_8479/06_2025/5u0p_8479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u0p_8479/06_2025/5u0p_8479.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 12745 2.51 5 N 3601 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20268 Number of models: 1 Model: "" Number of chains: 17 Chain: "N" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3777 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 19, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 130 Chain: "N" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1590 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1493 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Chain: "Q" Number of atoms: 3831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3831 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 485} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 164 Chain: "R" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1694 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 11, 'TRANS': 191} Chain: "T" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1455 Classifications: {'peptide': 179} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "K" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 769 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 949 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "G" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 965 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 181} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 667 Unresolved non-hydrogen angles: 838 Unresolved non-hydrogen dihedrals: 562 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 344 Chain: "U" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 608 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 217 Chain: "3" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 96} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 272 Chain: "I" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Chain: "2" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 388 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 73} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "S" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Chain breaks: 6 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "J" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 660 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'TRANS': 131} Chain breaks: 3 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 132 Planarities with less than four sites: {'UNK:plan-1': 132} Unresolved non-hydrogen planarities: 132 Time building chain proxies: 12.89, per 1000 atoms: 0.64 Number of scatterers: 20268 At special positions: 0 Unit cell: (158.51, 255.45, 131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 3867 8.00 N 3601 7.00 C 12745 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 Links applied TRANS " UNK N 880 " - " LYS N 879 " Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.6 seconds 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5738 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 19 sheets defined 67.4% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'N' and resid 87 through 93 removed outlier: 3.774A pdb=" N LYS N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 119 removed outlier: 3.523A pdb=" N SER N 109 " --> pdb=" O ARG N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 132 removed outlier: 4.128A pdb=" N SER N 130 " --> pdb=" O SER N 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG N 132 " --> pdb=" O GLY N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 172 removed outlier: 5.070A pdb=" N ARG N 166 " --> pdb=" O ASN N 162 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE N 167 " --> pdb=" O MET N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 254 removed outlier: 4.019A pdb=" N ARG N 237 " --> pdb=" O PRO N 233 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU N 241 " --> pdb=" O ARG N 237 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU N 242 " --> pdb=" O VAL N 238 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS N 243 " --> pdb=" O PHE N 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU N 244 " --> pdb=" O ILE N 240 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA N 249 " --> pdb=" O ASN N 245 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE N 252 " --> pdb=" O ILE N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 288 removed outlier: 3.727A pdb=" N TYR N 263 " --> pdb=" O LEU N 259 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE N 265 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE N 269 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS N 270 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN N 281 " --> pdb=" O LEU N 277 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 342 removed outlier: 3.510A pdb=" N ARG N 342 " --> pdb=" O SER N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 378 through 402 removed outlier: 3.733A pdb=" N LEU N 382 " --> pdb=" O ASP N 378 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU N 383 " --> pdb=" O ALA N 379 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 453 Processing helix chain 'N' and resid 453 through 459 Processing helix chain 'N' and resid 465 through 484 removed outlier: 3.793A pdb=" N ILE N 476 " --> pdb=" O TYR N 472 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN N 477 " --> pdb=" O PHE N 473 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU N 482 " --> pdb=" O THR N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 550 through 576 removed outlier: 4.004A pdb=" N LEU N 559 " --> pdb=" O SER N 555 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER N 560 " --> pdb=" O PHE N 556 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU N 563 " --> pdb=" O LEU N 559 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS N 576 " --> pdb=" O VAL N 572 " (cutoff:3.500A) Processing helix chain 'N' and resid 884 through 900 removed outlier: 3.929A pdb=" N UNK N 889 " --> pdb=" O UNK N 885 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N UNK N 890 " --> pdb=" O UNK N 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.872A pdb=" N LEU F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 59 removed outlier: 3.553A pdb=" N MET F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 120 through 142 removed outlier: 3.504A pdb=" N LEU F 124 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 211 removed outlier: 3.827A pdb=" N MET F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 37 removed outlier: 3.509A pdb=" N LYS H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 65 removed outlier: 3.604A pdb=" N ILE H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 74 removed outlier: 3.730A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 95 removed outlier: 3.607A pdb=" N THR H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.941A pdb=" N GLU H 113 " --> pdb=" O ASN H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 151 removed outlier: 3.722A pdb=" N GLN H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 148 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR H 151 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 198 removed outlier: 3.964A pdb=" N ALA H 178 " --> pdb=" O GLU H 174 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR H 179 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 12 Processing helix chain 'Q' and resid 13 through 19 Processing helix chain 'Q' and resid 29 through 39 removed outlier: 4.633A pdb=" N GLN Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 59 removed outlier: 3.934A pdb=" N ASP Q 50 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU Q 54 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 65 removed outlier: 3.949A pdb=" N ILE Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 76 removed outlier: 3.636A pdb=" N GLU Q 75 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 91 removed outlier: 3.846A pdb=" N THR Q 84 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU Q 85 " --> pdb=" O GLU Q 81 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP Q 86 " --> pdb=" O PHE Q 82 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER Q 87 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 95 removed outlier: 4.099A pdb=" N GLU Q 95 " --> pdb=" O ASN Q 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 92 through 95' Processing helix chain 'Q' and resid 102 through 131 removed outlier: 3.818A pdb=" N GLU Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA Q 122 " --> pdb=" O GLU Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 141 removed outlier: 3.594A pdb=" N ILE Q 141 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 147 Processing helix chain 'Q' and resid 165 through 214 removed outlier: 4.129A pdb=" N ALA Q 169 " --> pdb=" O LYS Q 165 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS Q 176 " --> pdb=" O ALA Q 172 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU Q 203 " --> pdb=" O GLU Q 199 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR Q 204 " --> pdb=" O THR Q 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR Q 205 " --> pdb=" O GLU Q 201 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR Q 206 " --> pdb=" O HIS Q 202 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU Q 207 " --> pdb=" O GLU Q 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA Q 214 " --> pdb=" O LYS Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 321 removed outlier: 3.611A pdb=" N LYS Q 296 " --> pdb=" O SER Q 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN Q 319 " --> pdb=" O LEU Q 315 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER Q 320 " --> pdb=" O GLN Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 322 through 325 Processing helix chain 'Q' and resid 377 through 404 removed outlier: 3.672A pdb=" N ALA Q 393 " --> pdb=" O LEU Q 389 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS Q 394 " --> pdb=" O ASN Q 390 " (cutoff:3.500A) Processing helix chain 'Q' and resid 409 through 414 removed outlier: 3.825A pdb=" N LEU Q 413 " --> pdb=" O GLN Q 409 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR Q 414 " --> pdb=" O GLN Q 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 409 through 414' Processing helix chain 'Q' and resid 425 through 447 removed outlier: 3.644A pdb=" N TYR Q 432 " --> pdb=" O LEU Q 428 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 removed outlier: 3.664A pdb=" N LYS Q 462 " --> pdb=" O PRO Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 473 removed outlier: 3.536A pdb=" N ASN Q 471 " --> pdb=" O LEU Q 467 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU Q 473 " --> pdb=" O LEU Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 522 through 543 removed outlier: 3.592A pdb=" N VAL Q 526 " --> pdb=" O SER Q 522 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS Q 533 " --> pdb=" O TYR Q 529 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER Q 538 " --> pdb=" O ILE Q 534 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 24 removed outlier: 3.657A pdb=" N VAL R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS R 24 " --> pdb=" O ASN R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 76 Processing helix chain 'R' and resid 110 through 116 removed outlier: 4.068A pdb=" N GLU R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 197 Processing helix chain 'R' and resid 198 through 200 No H-bonds generated for 'chain 'R' and resid 198 through 200' Processing helix chain 'T' and resid 14 through 22 Proline residue: T 20 - end of helix Processing helix chain 'T' and resid 79 through 87 removed outlier: 3.692A pdb=" N ILE T 83 " --> pdb=" O GLU T 79 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 138 Processing helix chain 'T' and resid 139 through 146 removed outlier: 3.782A pdb=" N PHE T 146 " --> pdb=" O ILE T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 175 through 186 removed outlier: 3.789A pdb=" N LEU T 179 " --> pdb=" O SER T 175 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE T 182 " --> pdb=" O LEU T 178 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS T 183 " --> pdb=" O LEU T 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 189 No H-bonds generated for 'chain 'T' and resid 187 through 189' Processing helix chain 'K' and resid 17 through 29 removed outlier: 4.363A pdb=" N VAL K 21 " --> pdb=" O ASP K 17 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 47 removed outlier: 4.620A pdb=" N ASP K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER K 36 " --> pdb=" O PRO K 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE K 45 " --> pdb=" O CYS K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 82 removed outlier: 3.718A pdb=" N LEU K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 68 " --> pdb=" O THR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 111 Processing helix chain 'V' and resid 6 through 39 removed outlier: 3.801A pdb=" N LEU V 10 " --> pdb=" O PHE V 6 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE V 35 " --> pdb=" O ARG V 31 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU V 36 " --> pdb=" O PHE V 32 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 83 removed outlier: 4.030A pdb=" N ALA V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Proline residue: V 51 - end of helix removed outlier: 3.770A pdb=" N TYR V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 112 Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.784A pdb=" N UNK D 19 " --> pdb=" O UNK D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 40 Processing helix chain 'D' and resid 40 through 87 removed outlier: 4.029A pdb=" N UNK D 44 " --> pdb=" O UNK D 40 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N UNK D 62 " --> pdb=" O UNK D 58 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N UNK D 63 " --> pdb=" O UNK D 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N UNK D 64 " --> pdb=" O UNK D 60 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK D 81 " --> pdb=" O UNK D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'G' and resid 18 through 23 removed outlier: 3.989A pdb=" N LYS G 21 " --> pdb=" O PRO G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 38 removed outlier: 3.538A pdb=" N ILE G 28 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 31 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.021A pdb=" N PHE G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.899A pdb=" N ASP G 79 " --> pdb=" O GLN G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 222 through 240 removed outlier: 4.119A pdb=" N GLU G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU G 230 " --> pdb=" O ARG G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 245 removed outlier: 3.799A pdb=" N LEU G 244 " --> pdb=" O ASN G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 258 removed outlier: 3.993A pdb=" N SER G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 266 removed outlier: 3.914A pdb=" N ILE G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 316 Proline residue: G 278 - end of helix removed outlier: 3.818A pdb=" N SER G 281 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU G 290 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS G 291 " --> pdb=" O MET G 287 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 293 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN G 299 " --> pdb=" O HIS G 295 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL G 300 " --> pdb=" O GLU G 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG G 304 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THR G 305 " --> pdb=" O GLU G 301 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG G 308 " --> pdb=" O ARG G 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN G 309 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 330 Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'U' and resid 4 through 11 removed outlier: 3.660A pdb=" N LEU U 8 " --> pdb=" O ARG U 4 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN U 9 " --> pdb=" O CYS U 5 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP U 10 " --> pdb=" O THR U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 22 removed outlier: 3.957A pdb=" N THR U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE U 19 " --> pdb=" O VAL U 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR U 20 " --> pdb=" O ALA U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 25 No H-bonds generated for 'chain 'U' and resid 23 through 25' Processing helix chain 'U' and resid 27 through 31 Processing helix chain 'U' and resid 51 through 79 removed outlier: 3.963A pdb=" N GLN U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE U 56 " --> pdb=" O GLU U 52 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL U 66 " --> pdb=" O ALA U 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE U 69 " --> pdb=" O LEU U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 137 removed outlier: 3.646A pdb=" N GLU U 91 " --> pdb=" O LYS U 87 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU U 102 " --> pdb=" O ASN U 98 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU U 105 " --> pdb=" O GLU U 101 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU U 106 " --> pdb=" O GLU U 102 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU U 111 " --> pdb=" O ARG U 107 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER U 112 " --> pdb=" O LYS U 108 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP U 116 " --> pdb=" O SER U 112 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU U 117 " --> pdb=" O GLU U 113 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN U 120 " --> pdb=" O ASP U 116 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS U 133 " --> pdb=" O GLY U 129 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL U 134 " --> pdb=" O ARG U 130 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU U 135 " --> pdb=" O LEU U 131 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 8 Processing helix chain '3' and resid 15 through 25 removed outlier: 4.067A pdb=" N GLU 3 20 " --> pdb=" O ARG 3 16 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU 3 21 " --> pdb=" O PHE 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 29 Processing helix chain '3' and resid 31 through 36 Processing helix chain '3' and resid 45 through 53 removed outlier: 4.023A pdb=" N GLN 3 49 " --> pdb=" O GLU 3 45 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 58 Processing helix chain '3' and resid 67 through 79 removed outlier: 4.429A pdb=" N CYS 3 71 " --> pdb=" O ILE 3 67 " (cutoff:3.500A) Processing helix chain '3' and resid 90 through 92 No H-bonds generated for 'chain '3' and resid 90 through 92' Processing helix chain '3' and resid 93 through 99 removed outlier: 3.892A pdb=" N ASN 3 97 " --> pdb=" O SER 3 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP 3 98 " --> pdb=" O LYS 3 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 58 removed outlier: 4.069A pdb=" N ILE I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG I 54 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 88 removed outlier: 3.827A pdb=" N VAL I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS I 73 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE I 76 " --> pdb=" O GLU I 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE I 77 " --> pdb=" O LYS I 73 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 Processing helix chain 'I' and resid 111 through 114 Processing helix chain 'I' and resid 115 through 121 Processing helix chain '2' and resid 2 through 22 Processing helix chain '2' and resid 32 through 45 Proline residue: 2 42 - end of helix Processing helix chain '2' and resid 62 through 70 Processing helix chain 'S' and resid 72 through 82 Processing helix chain 'S' and resid 252 through 265 Processing helix chain 'S' and resid 272 through 287 removed outlier: 3.580A pdb=" N UNK S 287 " --> pdb=" O UNK S 283 " (cutoff:3.500A) Processing helix chain 'S' and resid 302 through 321 Processing helix chain 'S' and resid 332 through 348 Processing helix chain 'S' and resid 352 through 364 removed outlier: 3.833A pdb=" N UNK S 356 " --> pdb=" O UNK S 352 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N UNK S 357 " --> pdb=" O UNK S 353 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK S 362 " --> pdb=" O UNK S 358 " (cutoff:3.500A) Processing helix chain 'S' and resid 382 through 399 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 20 through 22 No H-bonds generated for 'chain 'J' and resid 20 through 22' Processing helix chain 'J' and resid 26 through 55 removed outlier: 3.706A pdb=" N UNK J 31 " --> pdb=" O UNK J 27 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK J 34 " --> pdb=" O UNK J 30 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N UNK J 40 " --> pdb=" O UNK J 36 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N UNK J 43 " --> pdb=" O UNK J 39 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N UNK J 44 " --> pdb=" O UNK J 40 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N UNK J 52 " --> pdb=" O UNK J 48 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N UNK J 53 " --> pdb=" O UNK J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 204 Processing helix chain 'J' and resid 311 through 341 removed outlier: 3.801A pdb=" N UNK J 330 " --> pdb=" O UNK J 326 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N UNK J 335 " --> pdb=" O UNK J 331 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N UNK J 338 " --> pdb=" O UNK J 334 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK J 339 " --> pdb=" O UNK J 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 187 through 190 removed outlier: 6.814A pdb=" N SER N 198 " --> pdb=" O VAL N 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 307 through 308 Processing sheet with id=AA3, first strand: chain 'N' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'N' and resid 415 through 416 removed outlier: 3.733A pdb=" N LEU N 415 " --> pdb=" O ASN N 422 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU N 423 " --> pdb=" O VAL N 436 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE N 425 " --> pdb=" O ARG N 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 520 through 522 removed outlier: 3.696A pdb=" N SER N 528 " --> pdb=" O ASN N 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 76 through 79 removed outlier: 6.861A pdb=" N ILE F 91 " --> pdb=" O VAL F 107 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL F 107 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS F 93 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE F 109 " --> pdb=" O TYR F 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR F 116 " --> pdb=" O PHE F 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 148 through 150 Processing sheet with id=AA8, first strand: chain 'Q' and resid 218 through 220 removed outlier: 6.184A pdb=" N LEU Q 227 " --> pdb=" O ILE Q 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 277 through 281 removed outlier: 6.368A pdb=" N ILE Q 270 " --> pdb=" O ILE Q 278 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER Q 280 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE Q 268 " --> pdb=" O SER Q 280 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 327 through 328 Processing sheet with id=AB2, first strand: chain 'Q' and resid 454 through 455 removed outlier: 3.724A pdb=" N SER Q 481 " --> pdb=" O MET Q 455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id=AB4, first strand: chain 'R' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'R' and resid 8 through 10 removed outlier: 3.799A pdb=" N LEU R 129 " --> pdb=" O ILE R 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 8 through 10 removed outlier: 3.799A pdb=" N LEU R 129 " --> pdb=" O ILE R 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 102 through 104 removed outlier: 3.919A pdb=" N LEU R 104 " --> pdb=" O TRP R 78 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TRP R 78 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU R 56 " --> pdb=" O TYR R 39 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR R 39 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'T' and resid 57 through 58 removed outlier: 3.788A pdb=" N LYS T 57 " --> pdb=" O HIS T 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS T 33 " --> pdb=" O LYS T 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 113 through 114 1188 hydrogen bonds defined for protein. 3423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 6.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6830 1.33 - 1.45: 2525 1.45 - 1.57: 11128 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 20569 Sorted by residual: bond pdb=" C GLY T 100 " pdb=" O GLY T 100 " ideal model delta sigma weight residual 1.235 1.545 -0.310 1.35e-02 5.49e+03 5.28e+02 bond pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 1.332 1.576 -0.244 1.40e-02 5.10e+03 3.03e+02 bond pdb=" N SER T 101 " pdb=" CA SER T 101 " ideal model delta sigma weight residual 1.457 1.545 -0.087 1.29e-02 6.01e+03 4.57e+01 bond pdb=" CA GLY T 100 " pdb=" C GLY T 100 " ideal model delta sigma weight residual 1.514 1.591 -0.077 1.41e-02 5.03e+03 2.98e+01 bond pdb=" N PRO N 194 " pdb=" CD PRO N 194 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 20564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 27955 5.48 - 10.95: 116 10.95 - 16.43: 6 16.43 - 21.90: 1 21.90 - 27.38: 1 Bond angle restraints: 28079 Sorted by residual: angle pdb=" O GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 122.70 102.99 19.71 1.30e+00 5.92e-01 2.30e+02 angle pdb=" CA GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 116.69 144.07 -27.38 2.04e+00 2.40e-01 1.80e+02 angle pdb=" C LYS N 301 " pdb=" N PRO N 302 " pdb=" CA PRO N 302 " ideal model delta sigma weight residual 120.38 107.99 12.39 1.03e+00 9.43e-01 1.45e+02 angle pdb=" C LYS R 153 " pdb=" N PRO R 154 " pdb=" CA PRO R 154 " ideal model delta sigma weight residual 119.66 126.31 -6.65 7.20e-01 1.93e+00 8.53e+01 angle pdb=" CA PRO N 194 " pdb=" N PRO N 194 " pdb=" CD PRO N 194 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.25e+01 ... (remaining 28074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 12100 16.39 - 32.78: 232 32.78 - 49.17: 54 49.17 - 65.56: 7 65.56 - 81.95: 14 Dihedral angle restraints: 12407 sinusoidal: 3720 harmonic: 8687 Sorted by residual: dihedral pdb=" CA GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " pdb=" CA SER T 101 " ideal model delta harmonic sigma weight residual -180.00 -139.33 -40.67 0 5.00e+00 4.00e-02 6.62e+01 dihedral pdb=" N SER T 101 " pdb=" C SER T 101 " pdb=" CA SER T 101 " pdb=" CB SER T 101 " ideal model delta harmonic sigma weight residual 122.80 102.92 19.88 0 2.50e+00 1.60e-01 6.32e+01 dihedral pdb=" CA ASN R 47 " pdb=" C ASN R 47 " pdb=" N LEU R 48 " pdb=" CA LEU R 48 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 12404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 3372 0.132 - 0.265: 30 0.265 - 0.397: 1 0.397 - 0.529: 0 0.529 - 0.662: 1 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA SER T 101 " pdb=" N SER T 101 " pdb=" C SER T 101 " pdb=" CB SER T 101 " both_signs ideal model delta sigma weight residual False 2.51 3.17 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA PRO N 852 " pdb=" N PRO N 852 " pdb=" C PRO N 852 " pdb=" CB PRO N 852 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA PRO N 137 " pdb=" N PRO N 137 " pdb=" C PRO N 137 " pdb=" CB PRO N 137 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 3401 not shown) Planarity restraints: 3678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY T 100 " -0.063 2.00e-02 2.50e+03 9.37e-02 8.77e+01 pdb=" C GLY T 100 " 0.161 2.00e-02 2.50e+03 pdb=" O GLY T 100 " -0.036 2.00e-02 2.50e+03 pdb=" N SER T 101 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 256 " 0.082 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO N 257 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO N 257 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO N 257 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL N 193 " -0.088 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO N 194 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO N 194 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO N 194 " -0.062 5.00e-02 4.00e+02 ... (remaining 3675 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 21 2.21 - 2.88: 7915 2.88 - 3.56: 31944 3.56 - 4.23: 45274 4.23 - 4.90: 72783 Nonbonded interactions: 157937 Sorted by model distance: nonbonded pdb=" O PHE T 30 " pdb=" O GLY T 100 " model vdw 1.541 3.040 nonbonded pdb=" O PRO N 194 " pdb=" OD1 ASN N 195 " model vdw 1.903 3.040 nonbonded pdb=" O SER Q 167 " pdb=" OG1 THR Q 170 " model vdw 2.120 3.040 nonbonded pdb=" O TRP Q 444 " pdb=" NH1 ARG Q 448 " model vdw 2.136 3.120 nonbonded pdb=" O CYS N 475 " pdb=" OG1 THR N 478 " model vdw 2.152 3.040 ... (remaining 157932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'J' and resid 11 through 342) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 48.150 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 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 : 0.007 0.310 20570 Z= 0.437 Angle : 1.188 27.377 28082 Z= 0.823 Chirality : 0.048 0.662 3404 Planarity : 0.005 0.127 3677 Dihedral : 8.616 81.954 6666 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 3.45 % Allowed : 8.34 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2495 helix: -2.00 (0.10), residues: 1175 sheet: -3.33 (0.26), residues: 272 loop : 0.09 (0.23), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 362 HIS 0.007 0.001 HIS N 364 PHE 0.025 0.002 PHE H 50 TYR 0.021 0.002 TYR R 39 ARG 0.013 0.001 ARG N 166 Details of bonding type rmsd link_TRANS : bond 0.00059 ( 1) link_TRANS : angle 0.15810 ( 3) hydrogen bonds : bond 0.14878 ( 1173) hydrogen bonds : angle 9.08948 ( 3423) covalent geometry : bond 0.00651 (20569) covalent geometry : angle 1.18797 (28079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 349 THR cc_start: 0.8560 (p) cc_final: 0.8206 (t) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.4124 time to fit residues: 141.8011 Evaluate side-chains 112 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 355 HIS N 364 HIS N 380 GLN N 403 HIS ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 HIS F 49 ASN F 112 ASN H 47 HIS H 62 ASN H 63 ASN ** Q 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 377 GLN R 51 GLN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN R 163 GLN T 184 GLN K 75 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.052872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.039724 restraints weight = 259910.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.040540 restraints weight = 202652.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.040619 restraints weight = 151658.957| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20570 Z= 0.173 Angle : 0.734 12.067 28082 Z= 0.393 Chirality : 0.041 0.203 3404 Planarity : 0.005 0.085 3677 Dihedral : 5.726 30.962 3025 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.22 % Favored : 90.94 % Rotamer: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2495 helix: -0.40 (0.13), residues: 1209 sheet: -2.96 (0.25), residues: 288 loop : -0.98 (0.22), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 362 HIS 0.010 0.002 HIS N 545 PHE 0.026 0.002 PHE F 136 TYR 0.032 0.002 TYR Q 104 ARG 0.029 0.001 ARG F 17 Details of bonding type rmsd link_TRANS : bond 0.00154 ( 1) link_TRANS : angle 0.39812 ( 3) hydrogen bonds : bond 0.04124 ( 1173) hydrogen bonds : angle 6.00057 ( 3423) covalent geometry : bond 0.00349 (20569) covalent geometry : angle 0.73451 (28079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 380 GLN cc_start: 0.9086 (mt0) cc_final: 0.8742 (tt0) REVERT: F 65 ASP cc_start: 0.8838 (t0) cc_final: 0.8483 (m-30) REVERT: Q 308 MET cc_start: 0.9013 (mtp) cc_final: 0.8729 (mtp) REVERT: Q 381 LEU cc_start: 0.9491 (tt) cc_final: 0.9254 (mt) REVERT: Q 485 MET cc_start: 0.8736 (tmm) cc_final: 0.8364 (tmm) REVERT: R 80 MET cc_start: 0.8976 (tpp) cc_final: 0.8664 (tpp) REVERT: T 77 GLU cc_start: 0.8745 (pp20) cc_final: 0.8283 (pm20) REVERT: V 34 ASP cc_start: 0.9428 (m-30) cc_final: 0.9081 (m-30) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.3646 time to fit residues: 88.0818 Evaluate side-chains 110 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 46 optimal weight: 20.0000 chunk 234 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 243 HIS N 273 GLN ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 405 ASN N 418 HIS N 469 ASN F 69 GLN F 152 GLN F 204 GLN H 18 HIS H 56 GLN H 58 HIS H 62 ASN H 63 ASN Q 302 GLN Q 447 GLN Q 518 ASN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 ASN T 22 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.051774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.038607 restraints weight = 262538.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.039395 restraints weight = 203724.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.039384 restraints weight = 162540.547| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20570 Z= 0.169 Angle : 0.672 13.687 28082 Z= 0.358 Chirality : 0.039 0.198 3404 Planarity : 0.004 0.081 3677 Dihedral : 5.323 30.856 3025 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.94 % Favored : 90.22 % Rotamer: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2495 helix: 0.29 (0.14), residues: 1225 sheet: -3.06 (0.25), residues: 283 loop : -1.35 (0.22), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 527 HIS 0.009 0.001 HIS R 172 PHE 0.015 0.002 PHE N 340 TYR 0.026 0.002 TYR Q 104 ARG 0.005 0.001 ARG N 166 Details of bonding type rmsd link_TRANS : bond 0.00157 ( 1) link_TRANS : angle 0.37382 ( 3) hydrogen bonds : bond 0.03739 ( 1173) hydrogen bonds : angle 5.44930 ( 3423) covalent geometry : bond 0.00351 (20569) covalent geometry : angle 0.67231 (28079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 335 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8742 (tp-100) REVERT: N 380 GLN cc_start: 0.9234 (mt0) cc_final: 0.8885 (tt0) REVERT: F 25 MET cc_start: 0.8340 (mpp) cc_final: 0.8066 (pmm) REVERT: F 65 ASP cc_start: 0.8890 (t0) cc_final: 0.8598 (m-30) REVERT: F 117 MET cc_start: 0.6079 (mmp) cc_final: 0.5409 (mmp) REVERT: H 145 MET cc_start: 0.9632 (ptt) cc_final: 0.9331 (ppp) REVERT: Q 246 MET cc_start: 0.8397 (tpt) cc_final: 0.8154 (tpp) REVERT: Q 308 MET cc_start: 0.9053 (mtp) cc_final: 0.8785 (mtp) REVERT: Q 485 MET cc_start: 0.8814 (tmm) cc_final: 0.8376 (tmm) REVERT: R 80 MET cc_start: 0.8950 (tpp) cc_final: 0.8639 (tpp) REVERT: T 77 GLU cc_start: 0.8837 (pp20) cc_final: 0.8454 (pm20) REVERT: V 34 ASP cc_start: 0.9356 (m-30) cc_final: 0.9118 (m-30) REVERT: V 90 PHE cc_start: 0.7634 (p90) cc_final: 0.7413 (p90) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.3860 time to fit residues: 77.6913 Evaluate side-chains 95 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 GLN N 381 HIS F 49 ASN F 207 HIS H 58 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.050304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.037409 restraints weight = 267797.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.038202 restraints weight = 212552.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.038008 restraints weight = 177144.179| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20570 Z= 0.221 Angle : 0.697 11.945 28082 Z= 0.372 Chirality : 0.040 0.181 3404 Planarity : 0.004 0.076 3677 Dihedral : 5.329 28.029 3025 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.90 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2495 helix: 0.68 (0.15), residues: 1222 sheet: -2.94 (0.24), residues: 298 loop : -1.55 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 21 HIS 0.008 0.001 HIS T 33 PHE 0.024 0.002 PHE F 136 TYR 0.023 0.002 TYR Q 104 ARG 0.007 0.001 ARG H 19 Details of bonding type rmsd link_TRANS : bond 0.00212 ( 1) link_TRANS : angle 0.32798 ( 3) hydrogen bonds : bond 0.03675 ( 1173) hydrogen bonds : angle 5.20021 ( 3423) covalent geometry : bond 0.00446 (20569) covalent geometry : angle 0.69708 (28079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 335 GLN cc_start: 0.9022 (tp-100) cc_final: 0.8693 (tp-100) REVERT: N 434 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7636 (ttp80) REVERT: F 65 ASP cc_start: 0.9009 (t0) cc_final: 0.8636 (m-30) REVERT: F 117 MET cc_start: 0.6924 (mmp) cc_final: 0.6116 (mmp) REVERT: H 145 MET cc_start: 0.9612 (ptt) cc_final: 0.9338 (ppp) REVERT: Q 308 MET cc_start: 0.9019 (mtp) cc_final: 0.8638 (mtp) REVERT: Q 485 MET cc_start: 0.8837 (tmm) cc_final: 0.8426 (tmm) REVERT: R 80 MET cc_start: 0.8975 (tpp) cc_final: 0.8605 (tpp) REVERT: T 77 GLU cc_start: 0.8906 (pp20) cc_final: 0.8499 (pm20) REVERT: V 32 PHE cc_start: 0.9616 (t80) cc_final: 0.9335 (t80) REVERT: V 34 ASP cc_start: 0.9370 (m-30) cc_final: 0.9156 (m-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3718 time to fit residues: 66.3870 Evaluate side-chains 91 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 159 optimal weight: 0.0770 chunk 179 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 chunk 269 optimal weight: 50.0000 chunk 281 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 164 optimal weight: 0.0270 chunk 71 optimal weight: 0.8980 chunk 266 optimal weight: 50.0000 chunk 274 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS Q 447 GLN R 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.051380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.038269 restraints weight = 261209.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.039338 restraints weight = 204958.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.039255 restraints weight = 147324.254| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20570 Z= 0.127 Angle : 0.617 12.199 28082 Z= 0.326 Chirality : 0.039 0.173 3404 Planarity : 0.004 0.076 3677 Dihedral : 4.977 27.177 3025 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.54 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2495 helix: 0.96 (0.15), residues: 1225 sheet: -2.64 (0.26), residues: 305 loop : -1.62 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 21 HIS 0.005 0.001 HIS V 59 PHE 0.016 0.001 PHE H 30 TYR 0.020 0.001 TYR Q 104 ARG 0.013 0.001 ARG V 31 Details of bonding type rmsd link_TRANS : bond 0.00158 ( 1) link_TRANS : angle 0.33531 ( 3) hydrogen bonds : bond 0.03271 ( 1173) hydrogen bonds : angle 4.77624 ( 3423) covalent geometry : bond 0.00257 (20569) covalent geometry : angle 0.61738 (28079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 335 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8651 (tp-100) REVERT: N 434 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7642 (ttp80) REVERT: F 111 CYS cc_start: 0.9077 (t) cc_final: 0.8849 (t) REVERT: Q 485 MET cc_start: 0.8772 (tmm) cc_final: 0.8302 (tmm) REVERT: T 77 GLU cc_start: 0.8788 (pp20) cc_final: 0.8431 (pm20) REVERT: V 32 PHE cc_start: 0.9534 (t80) cc_final: 0.9063 (t80) REVERT: V 47 TYR cc_start: 0.9407 (m-80) cc_final: 0.8388 (m-80) REVERT: V 72 ASP cc_start: 0.8811 (m-30) cc_final: 0.8588 (m-30) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3397 time to fit residues: 65.5870 Evaluate side-chains 96 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 38 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 264 optimal weight: 50.0000 chunk 96 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 153 GLN N 159 HIS ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 HIS ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN R 100 ASN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.048911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.036309 restraints weight = 271951.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.036904 restraints weight = 212593.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.036986 restraints weight = 179461.367| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 20570 Z= 0.255 Angle : 0.751 11.820 28082 Z= 0.395 Chirality : 0.040 0.199 3404 Planarity : 0.005 0.080 3677 Dihedral : 5.264 26.486 3025 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.22 % Favored : 90.18 % Rotamer: Outliers : 0.06 % Allowed : 1.93 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2495 helix: 0.96 (0.15), residues: 1231 sheet: -2.54 (0.26), residues: 301 loop : -1.77 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP N 527 HIS 0.010 0.002 HIS T 33 PHE 0.029 0.002 PHE F 136 TYR 0.029 0.003 TYR R 39 ARG 0.017 0.001 ARG R 40 Details of bonding type rmsd link_TRANS : bond 0.00237 ( 1) link_TRANS : angle 0.34936 ( 3) hydrogen bonds : bond 0.03684 ( 1173) hydrogen bonds : angle 4.95079 ( 3423) covalent geometry : bond 0.00528 (20569) covalent geometry : angle 0.75128 (28079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 2.131 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: N 434 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7779 (ttp80) REVERT: F 117 MET cc_start: 0.7121 (mmp) cc_final: 0.6217 (mmt) REVERT: Q 246 MET cc_start: 0.8781 (tpt) cc_final: 0.8455 (tpt) REVERT: Q 485 MET cc_start: 0.8719 (tmm) cc_final: 0.8119 (tmm) REVERT: T 77 GLU cc_start: 0.9080 (pp20) cc_final: 0.8712 (pm20) REVERT: V 32 PHE cc_start: 0.9567 (t80) cc_final: 0.9130 (t80) REVERT: V 72 ASP cc_start: 0.8751 (m-30) cc_final: 0.8521 (m-30) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.3291 time to fit residues: 55.8429 Evaluate side-chains 80 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 234 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 220 ASN Q 447 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.050026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.037220 restraints weight = 263559.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.038148 restraints weight = 203553.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.038089 restraints weight = 165023.967| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20570 Z= 0.134 Angle : 0.619 12.191 28082 Z= 0.328 Chirality : 0.038 0.164 3404 Planarity : 0.004 0.079 3677 Dihedral : 4.963 27.140 3025 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.22 % Favored : 91.14 % Rotamer: Outliers : 0.06 % Allowed : 1.14 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2495 helix: 1.21 (0.15), residues: 1234 sheet: -2.36 (0.27), residues: 304 loop : -1.76 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 527 HIS 0.005 0.001 HIS N 326 PHE 0.015 0.001 PHE N 340 TYR 0.017 0.001 TYR N 309 ARG 0.004 0.001 ARG R 90 Details of bonding type rmsd link_TRANS : bond 0.00184 ( 1) link_TRANS : angle 0.31401 ( 3) hydrogen bonds : bond 0.03220 ( 1173) hydrogen bonds : angle 4.61473 ( 3423) covalent geometry : bond 0.00274 (20569) covalent geometry : angle 0.61865 (28079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 2.310 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: N 434 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8177 (ttp80) REVERT: Q 116 GLN cc_start: 0.9619 (tt0) cc_final: 0.9391 (tp-100) REVERT: Q 485 MET cc_start: 0.8773 (tmm) cc_final: 0.8358 (tmm) REVERT: R 80 MET cc_start: 0.8805 (tpt) cc_final: 0.8186 (tpt) REVERT: T 77 GLU cc_start: 0.8946 (pp20) cc_final: 0.8584 (pm20) REVERT: V 32 PHE cc_start: 0.9534 (t80) cc_final: 0.9065 (t80) REVERT: V 47 TYR cc_start: 0.9377 (m-80) cc_final: 0.8326 (m-80) REVERT: V 72 ASP cc_start: 0.8947 (m-30) cc_final: 0.8686 (m-30) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.3540 time to fit residues: 63.9752 Evaluate side-chains 92 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 278 optimal weight: 50.0000 chunk 233 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 260 optimal weight: 40.0000 chunk 243 optimal weight: 40.0000 chunk 164 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN F 162 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.047673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.035363 restraints weight = 277848.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.036154 restraints weight = 220956.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.036023 restraints weight = 171947.842| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20570 Z= 0.306 Angle : 0.824 11.848 28082 Z= 0.435 Chirality : 0.043 0.243 3404 Planarity : 0.005 0.077 3677 Dihedral : 5.490 28.163 3025 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.54 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2495 helix: 0.80 (0.15), residues: 1244 sheet: -2.21 (0.29), residues: 284 loop : -2.06 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP N 527 HIS 0.015 0.003 HIS T 33 PHE 0.026 0.003 PHE R 112 TYR 0.024 0.003 TYR H 77 ARG 0.013 0.001 ARG N 188 Details of bonding type rmsd link_TRANS : bond 0.00303 ( 1) link_TRANS : angle 0.39759 ( 3) hydrogen bonds : bond 0.03878 ( 1173) hydrogen bonds : angle 5.00410 ( 3423) covalent geometry : bond 0.00629 (20569) covalent geometry : angle 0.82369 (28079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 2.303 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: N 377 MET cc_start: 0.5956 (mtt) cc_final: 0.5393 (mpp) REVERT: N 434 ARG cc_start: 0.8451 (ttp80) cc_final: 0.7877 (ttp80) REVERT: F 117 MET cc_start: 0.6953 (mmp) cc_final: 0.6081 (mmt) REVERT: Q 113 MET cc_start: 0.9134 (mtm) cc_final: 0.8807 (ptm) REVERT: Q 246 MET cc_start: 0.8602 (tpt) cc_final: 0.8293 (tpp) REVERT: Q 485 MET cc_start: 0.8751 (tmm) cc_final: 0.8167 (tmm) REVERT: R 80 MET cc_start: 0.8808 (tpt) cc_final: 0.8183 (tpt) REVERT: T 77 GLU cc_start: 0.9071 (pp20) cc_final: 0.8691 (pm20) REVERT: V 72 ASP cc_start: 0.8741 (m-30) cc_final: 0.8531 (m-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3473 time to fit residues: 55.4923 Evaluate side-chains 82 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 105 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 151 optimal weight: 0.9980 chunk 254 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 284 GLN ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 429 ASN F 131 ASN H 62 ASN H 63 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.049430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.036827 restraints weight = 265887.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.037560 restraints weight = 201937.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.037533 restraints weight = 171661.671| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20570 Z= 0.130 Angle : 0.634 12.304 28082 Z= 0.333 Chirality : 0.039 0.253 3404 Planarity : 0.004 0.069 3677 Dihedral : 5.044 27.073 3025 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.18 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2495 helix: 1.23 (0.15), residues: 1240 sheet: -2.18 (0.29), residues: 291 loop : -1.93 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP N 527 HIS 0.005 0.001 HIS N 326 PHE 0.015 0.001 PHE N 340 TYR 0.014 0.001 TYR N 309 ARG 0.006 0.001 ARG N 188 Details of bonding type rmsd link_TRANS : bond 0.00252 ( 1) link_TRANS : angle 0.40666 ( 3) hydrogen bonds : bond 0.03198 ( 1173) hydrogen bonds : angle 4.49035 ( 3423) covalent geometry : bond 0.00264 (20569) covalent geometry : angle 0.63381 (28079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.314 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: N 377 MET cc_start: 0.6194 (mtt) cc_final: 0.5967 (mpp) REVERT: N 380 GLN cc_start: 0.9494 (mt0) cc_final: 0.8995 (tt0) REVERT: N 420 PHE cc_start: 0.8342 (p90) cc_final: 0.8096 (p90) REVERT: N 434 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8038 (ttp80) REVERT: F 25 MET cc_start: 0.8563 (ptp) cc_final: 0.8272 (pmm) REVERT: F 117 MET cc_start: 0.6386 (mmp) cc_final: 0.4169 (mpp) REVERT: Q 113 MET cc_start: 0.9158 (mtm) cc_final: 0.8800 (ptm) REVERT: Q 246 MET cc_start: 0.8775 (tpt) cc_final: 0.8489 (tpp) REVERT: Q 308 MET cc_start: 0.9040 (mtp) cc_final: 0.8806 (mtp) REVERT: Q 485 MET cc_start: 0.8761 (tmm) cc_final: 0.8266 (tmm) REVERT: R 80 MET cc_start: 0.8750 (tpt) cc_final: 0.8112 (mpp) REVERT: T 77 GLU cc_start: 0.9072 (pp20) cc_final: 0.8731 (pm20) REVERT: V 32 PHE cc_start: 0.9527 (t80) cc_final: 0.9022 (t80) REVERT: V 47 TYR cc_start: 0.9290 (m-80) cc_final: 0.8872 (m-80) REVERT: V 72 ASP cc_start: 0.8877 (m-30) cc_final: 0.8592 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3458 time to fit residues: 63.7723 Evaluate side-chains 89 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 157 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 66 optimal weight: 0.0000 chunk 247 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 250 optimal weight: 30.0000 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 447 GLN T 32 GLN ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.049308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.036734 restraints weight = 267323.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.037311 restraints weight = 209821.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.037521 restraints weight = 166414.401| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20570 Z= 0.130 Angle : 0.612 12.071 28082 Z= 0.324 Chirality : 0.039 0.276 3404 Planarity : 0.004 0.066 3677 Dihedral : 4.818 27.424 3025 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.38 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2495 helix: 1.38 (0.15), residues: 1237 sheet: -1.93 (0.30), residues: 281 loop : -1.94 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 527 HIS 0.005 0.001 HIS N 364 PHE 0.012 0.001 PHE N 340 TYR 0.016 0.001 TYR N 172 ARG 0.010 0.001 ARG N 188 Details of bonding type rmsd link_TRANS : bond 0.00244 ( 1) link_TRANS : angle 0.39505 ( 3) hydrogen bonds : bond 0.03058 ( 1173) hydrogen bonds : angle 4.36171 ( 3423) covalent geometry : bond 0.00271 (20569) covalent geometry : angle 0.61250 (28079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 3.276 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: N 377 MET cc_start: 0.6795 (mtt) cc_final: 0.5962 (mtt) REVERT: N 380 GLN cc_start: 0.9327 (mt0) cc_final: 0.9008 (tt0) REVERT: N 434 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8053 (ttp80) REVERT: F 25 MET cc_start: 0.8611 (ptp) cc_final: 0.8318 (pmm) REVERT: F 117 MET cc_start: 0.6356 (mmp) cc_final: 0.4141 (mpp) REVERT: Q 113 MET cc_start: 0.9091 (mtm) cc_final: 0.8844 (mtp) REVERT: Q 246 MET cc_start: 0.8772 (tpt) cc_final: 0.8478 (tpp) REVERT: Q 485 MET cc_start: 0.8740 (tmm) cc_final: 0.8231 (tmm) REVERT: R 80 MET cc_start: 0.8726 (tpt) cc_final: 0.8193 (mpp) REVERT: T 77 GLU cc_start: 0.9058 (pp20) cc_final: 0.8728 (pm20) REVERT: V 47 TYR cc_start: 0.9261 (m-80) cc_final: 0.8854 (m-80) REVERT: V 72 ASP cc_start: 0.8860 (m-30) cc_final: 0.8573 (m-30) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3566 time to fit residues: 60.8883 Evaluate side-chains 86 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 117 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 245 optimal weight: 0.7980 chunk 225 optimal weight: 40.0000 chunk 206 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 248 optimal weight: 40.0000 chunk 237 optimal weight: 50.0000 chunk 247 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.048611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.036176 restraints weight = 272361.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.037087 restraints weight = 211350.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.037036 restraints weight = 163606.884| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20570 Z= 0.161 Angle : 0.634 12.009 28082 Z= 0.335 Chirality : 0.038 0.281 3404 Planarity : 0.004 0.067 3677 Dihedral : 4.814 27.466 3025 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.42 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2495 helix: 1.46 (0.15), residues: 1236 sheet: -1.86 (0.31), residues: 278 loop : -1.93 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP N 527 HIS 0.008 0.001 HIS V 59 PHE 0.014 0.001 PHE N 340 TYR 0.018 0.002 TYR K 57 ARG 0.008 0.001 ARG V 31 Details of bonding type rmsd link_TRANS : bond 0.00254 ( 1) link_TRANS : angle 0.40956 ( 3) hydrogen bonds : bond 0.03120 ( 1173) hydrogen bonds : angle 4.35510 ( 3423) covalent geometry : bond 0.00337 (20569) covalent geometry : angle 0.63380 (28079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6038.20 seconds wall clock time: 105 minutes 31.32 seconds (6331.32 seconds total)