Starting phenix.real_space_refine (version: dev) on Thu Feb 23 13:25:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/02_2023/5u0p_8479.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/02_2023/5u0p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/02_2023/5u0p_8479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/02_2023/5u0p_8479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/02_2023/5u0p_8479.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/02_2023/5u0p_8479.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "N PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ARG 206": "NH1" <-> "NH2" Residue "T PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20268 Number of models: 1 Model: "" Number of chains: 16 Chain: "N" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3887 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'CIS': 19, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 478} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'UNK:plan-1': 22, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 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: 11.54, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.97 Conformation dependent library (CDL) restraints added in 3.0 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: 0.80 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: 5.94 Time building geometry restraints manager: 9.56 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: 6831 1.33 - 1.45: 2525 1.45 - 1.57: 11128 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 20570 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 20565 not shown) Histogram of bond angle deviations from ideal: 96.97 - 106.39: 469 106.39 - 115.81: 13225 115.81 - 125.23: 14124 125.23 - 134.65: 260 134.65 - 144.07: 4 Bond angle restraints: 28082 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 28077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 12100 16.39 - 32.78: 231 32.78 - 49.17: 54 49.17 - 65.56: 7 65.56 - 81.95: 13 Dihedral angle restraints: 12405 sinusoidal: 3718 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 12402 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 2.440 nonbonded pdb=" O TRP Q 444 " pdb=" NH1 ARG Q 448 " model vdw 2.136 2.520 nonbonded pdb=" O CYS N 475 " pdb=" OG1 THR N 478 " model vdw 2.152 2.440 ... (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 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 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. 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: 2.080 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: 0.010 Extract box with map and model: 11.100 Check model and map are aligned: 0.300 Process input model: 51.980 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 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= 0.402 Angle : 1.184 27.377 28082 Z= 0.819 Chirality : 0.048 0.662 3404 Planarity : 0.005 0.127 3678 Dihedral : 8.615 81.954 6667 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.530 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 outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.4200 time to fit residues: 144.0727 Evaluate side-chains 111 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 7.9990 chunk 216 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 258 optimal weight: 40.0000 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN H 18 HIS H 25 GLN H 47 HIS H 62 ASN H 63 ASN ** Q 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN Q 518 ASN R 51 GLN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN R 163 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 184 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 20570 Z= 0.207 Angle : 0.743 18.402 28082 Z= 0.376 Chirality : 0.040 0.207 3404 Planarity : 0.005 0.081 3678 Dihedral : 5.674 30.125 3026 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.98 % Favored : 91.06 % Rotamer Outliers : 0.06 % 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: -1.53 (0.16), residues: 2495 helix: -0.37 (0.13), residues: 1214 sheet: -2.94 (0.25), residues: 283 loop : -1.02 (0.22), residues: 998 *********************** 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 164 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 2.480 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 outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.3722 time to fit residues: 91.8280 Evaluate side-chains 110 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 259 optimal weight: 9.9990 chunk 280 optimal weight: 50.0000 chunk 230 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 208 optimal weight: 20.0000 overall best weight: 3.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 159 HIS ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 243 HIS N 273 GLN ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 405 ASN ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN H 63 ASN H 67 HIS Q 302 GLN Q 377 GLN Q 447 GLN Q 525 ASN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN R 178 ASN T 22 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 20570 Z= 0.325 Angle : 0.776 18.135 28082 Z= 0.390 Chirality : 0.039 0.186 3404 Planarity : 0.005 0.078 3678 Dihedral : 5.467 30.204 3026 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.98 % Favored : 90.14 % Rotamer Outliers : 0.06 % 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: -1.18 (0.17), residues: 2495 helix: 0.30 (0.14), residues: 1223 sheet: -3.10 (0.24), residues: 295 loop : -1.30 (0.22), residues: 977 *********************** 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 120 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 2.426 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 outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.3851 time to fit residues: 70.3556 Evaluate side-chains 84 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 260 optimal weight: 40.0000 chunk 275 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 469 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN H 63 ASN ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 GLN Q 447 GLN R 65 HIS ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 20570 Z= 0.245 Angle : 0.701 18.435 28082 Z= 0.348 Chirality : 0.038 0.168 3404 Planarity : 0.004 0.071 3678 Dihedral : 5.317 28.187 3026 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.54 % Favored : 90.78 % Rotamer Outliers : 0.06 % 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: -0.91 (0.17), residues: 2495 helix: 0.77 (0.15), residues: 1226 sheet: -2.86 (0.24), residues: 300 loop : -1.58 (0.21), residues: 969 *********************** 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 115 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.391 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 outliers start: 1 outliers final: 1 residues processed: 115 average time/residue: 0.3703 time to fit residues: 66.0474 Evaluate side-chains 85 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 2.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2277 time to fit residues: 3.7331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 140 optimal weight: 2.9990 chunk 247 optimal weight: 0.0770 chunk 69 optimal weight: 7.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 267 HIS ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** Q 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 20570 Z= 0.219 Angle : 0.679 18.320 28082 Z= 0.333 Chirality : 0.038 0.216 3404 Planarity : 0.004 0.071 3678 Dihedral : 5.094 27.188 3026 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.86 % Favored : 90.46 % Rotamer Outliers : 0.18 % 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: -0.66 (0.18), residues: 2495 helix: 1.10 (0.15), residues: 1223 sheet: -2.66 (0.26), residues: 296 loop : -1.68 (0.21), residues: 976 *********************** 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 115 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 2.457 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 outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 0.3540 time to fit residues: 63.3371 Evaluate side-chains 86 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 2.548 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2245 time to fit residues: 3.6188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 153 GLN ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 226 HIS ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** Q 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 20570 Z= 0.297 Angle : 0.728 18.358 28082 Z= 0.364 Chirality : 0.039 0.222 3404 Planarity : 0.004 0.073 3678 Dihedral : 5.244 26.369 3026 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.54 % Favored : 89.86 % Rotamer Outliers : 0.00 % 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: -0.72 (0.17), residues: 2495 helix: 1.06 (0.15), residues: 1236 sheet: -2.54 (0.26), residues: 299 loop : -1.81 (0.21), residues: 960 *********************** 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 105 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3027 time to fit residues: 52.6272 Evaluate side-chains 79 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 50.0000 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 232 optimal weight: 50.0000 chunk 153 optimal weight: 0.9990 chunk 274 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 126 optimal weight: 0.0570 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** Q 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20570 Z= 0.201 Angle : 0.673 18.756 28082 Z= 0.330 Chirality : 0.038 0.160 3404 Planarity : 0.004 0.061 3678 Dihedral : 5.053 26.358 3026 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.22 % Favored : 90.18 % Rotamer Outliers : 0.00 % 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: -0.49 (0.18), residues: 2495 helix: 1.31 (0.15), residues: 1240 sheet: -2.32 (0.27), residues: 280 loop : -1.87 (0.21), residues: 975 *********************** 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 109 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.495 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 outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3369 time to fit residues: 58.1633 Evaluate side-chains 82 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 215 optimal weight: 30.0000 chunk 249 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 380 GLN ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** Q 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20570 Z= 0.241 Angle : 0.692 18.549 28082 Z= 0.343 Chirality : 0.038 0.251 3404 Planarity : 0.004 0.063 3678 Dihedral : 5.083 28.636 3026 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.02 % Favored : 90.38 % Rotamer Outliers : 0.00 % 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: -0.42 (0.18), residues: 2495 helix: 1.38 (0.15), residues: 1242 sheet: -2.13 (0.28), residues: 280 loop : -1.94 (0.21), residues: 973 *********************** 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 109 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.718 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 outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3347 time to fit residues: 57.5925 Evaluate side-chains 81 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 50.0000 chunk 240 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 201 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 231 optimal weight: 50.0000 chunk 242 optimal weight: 30.0000 chunk 168 optimal weight: 0.9990 chunk 270 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 284 GLN ** N 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN ** Q 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** Q 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 20570 Z= 0.411 Angle : 0.876 18.517 28082 Z= 0.442 Chirality : 0.042 0.308 3404 Planarity : 0.005 0.061 3678 Dihedral : 5.692 30.314 3026 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.30 % Favored : 89.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % 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: -1.09 (0.17), residues: 2495 helix: 0.78 (0.15), residues: 1248 sheet: -2.26 (0.29), residues: 284 loop : -2.26 (0.21), residues: 963 *********************** 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 102 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3406 time to fit residues: 55.6525 Evaluate side-chains 77 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 283 optimal weight: 40.0000 chunk 261 optimal weight: 50.0000 chunk 226 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 174 optimal weight: 0.0000 chunk 138 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 overall best weight: 3.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN H 63 ASN ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** Q 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 20570 Z= 0.287 Angle : 0.752 18.630 28082 Z= 0.373 Chirality : 0.039 0.233 3404 Planarity : 0.004 0.061 3678 Dihedral : 5.480 29.390 3026 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.62 % Favored : 89.78 % Rotamer Outliers : 0.00 % 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: -0.77 (0.18), residues: 2495 helix: 1.10 (0.15), residues: 1244 sheet: -2.15 (0.29), residues: 297 loop : -2.16 (0.21), residues: 954 ********************** 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 99 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3335 time to fit residues: 53.9089 Evaluate side-chains 76 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 226 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 232 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 198 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN H 63 ASN ** Q 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** Q 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.047564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.035501 restraints weight = 276743.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.036202 restraints weight = 223031.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.036866 restraints weight = 168687.807| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 20570 Z= 0.241 Angle : 0.709 18.597 28082 Z= 0.348 Chirality : 0.039 0.229 3404 Planarity : 0.004 0.062 3678 Dihedral : 5.244 28.580 3026 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.38 % Favored : 89.98 % Rotamer Outliers : 0.00 % 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: -0.50 (0.18), residues: 2495 helix: 1.34 (0.15), residues: 1240 sheet: -2.02 (0.30), residues: 283 loop : -2.07 (0.21), residues: 972 =============================================================================== Job complete usr+sys time: 2948.20 seconds wall clock time: 55 minutes 30.88 seconds (3330.88 seconds total)