Starting phenix.real_space_refine on Thu Sep 18 21:37:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u0p_8479/09_2025/5u0p_8479.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u0p_8479/09_2025/5u0p_8479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u0p_8479/09_2025/5u0p_8479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u0p_8479/09_2025/5u0p_8479.map" model { file = "/net/cci-nas-00/data/ceres_data/5u0p_8479/09_2025/5u0p_8479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u0p_8479/09_2025/5u0p_8479.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 12745 2.51 5 N 3601 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20268 Number of models: 1 Model: "" Number of chains: 17 Chain: "N" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3777 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 19, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'PHE:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ASP:plan': 4, 'ARG:plan': 6, 'TYR:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 130 Chain: "N" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1590 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1493 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Chain: "Q" Number of atoms: 3831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3831 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 485} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 13, 'GLN:plan1': 7, 'ASN:plan1': 7, 'PHE:plan': 4, '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: {'PHE:plan': 9, 'TYR:plan': 6, 'ARG:plan': 12, 'GLU:plan': 18, 'ASN:plan1': 9, 'GLN:plan1': 8, 'ASP:plan': 6, 'TRP:plan': 1, 'HIS:plan': 6} 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: {'ARG:plan': 5, 'GLN:plan1': 12, 'ASP:plan': 7, 'GLU:plan': 11, 'PHE:plan': 6, 'TYR:plan': 2, 'HIS:plan': 4, 'ASN:plan1': 3} 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: {'GLU:plan': 12, 'TRP:plan': 4, 'ASP:plan': 6, 'ARG:plan': 4, 'PHE:plan': 7, 'GLN:plan1': 5, 'ASN:plan1': 5, 'TYR:plan': 9, 'HIS:plan': 2} 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: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 10, 'PHE:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} 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: {'GLU:plan': 8, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'HIS:plan': 6, 'ASN:plan1': 8, 'PHE:plan': 2, 'TYR:plan': 1} 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: 4.75, per 1000 atoms: 0.23 Number of scatterers: 20268 At special positions: 0 Unit cell: (158.51, 255.45, 131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 3867 8.00 N 3601 7.00 C 12745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK N 880 " - " LYS N 879 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 697.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.67 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: 3.41 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6830 1.33 - 1.45: 2525 1.45 - 1.57: 11128 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 20569 Sorted by residual: bond pdb=" C GLY T 100 " pdb=" O GLY T 100 " ideal model delta sigma weight residual 1.235 1.545 -0.310 1.35e-02 5.49e+03 5.28e+02 bond pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 1.332 1.576 -0.244 1.40e-02 5.10e+03 3.03e+02 bond pdb=" N SER T 101 " pdb=" CA SER T 101 " ideal model delta sigma weight residual 1.457 1.545 -0.087 1.29e-02 6.01e+03 4.57e+01 bond pdb=" CA GLY T 100 " pdb=" C GLY T 100 " ideal model delta sigma weight residual 1.514 1.591 -0.077 1.41e-02 5.03e+03 2.98e+01 bond pdb=" N PRO N 194 " pdb=" CD PRO N 194 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 20564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 27955 5.48 - 10.95: 116 10.95 - 16.43: 6 16.43 - 21.90: 1 21.90 - 27.38: 1 Bond angle restraints: 28079 Sorted by residual: angle pdb=" O GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 122.70 102.99 19.71 1.30e+00 5.92e-01 2.30e+02 angle pdb=" CA GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 116.69 144.07 -27.38 2.04e+00 2.40e-01 1.80e+02 angle pdb=" C LYS N 301 " pdb=" N PRO N 302 " pdb=" CA PRO N 302 " ideal model delta sigma weight residual 120.38 107.99 12.39 1.03e+00 9.43e-01 1.45e+02 angle pdb=" C LYS R 153 " pdb=" N PRO R 154 " pdb=" CA PRO R 154 " ideal model delta sigma weight residual 119.66 126.31 -6.65 7.20e-01 1.93e+00 8.53e+01 angle pdb=" CA PRO N 194 " pdb=" N PRO N 194 " pdb=" CD PRO N 194 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.25e+01 ... (remaining 28074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 12100 16.39 - 32.78: 232 32.78 - 49.17: 54 49.17 - 65.56: 7 65.56 - 81.95: 14 Dihedral angle restraints: 12407 sinusoidal: 3720 harmonic: 8687 Sorted by residual: dihedral pdb=" CA GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " pdb=" CA SER T 101 " ideal model delta harmonic sigma weight residual -180.00 -139.33 -40.67 0 5.00e+00 4.00e-02 6.62e+01 dihedral pdb=" N SER T 101 " pdb=" C SER T 101 " pdb=" CA SER T 101 " pdb=" CB SER T 101 " ideal model delta harmonic sigma weight residual 122.80 102.92 19.88 0 2.50e+00 1.60e-01 6.32e+01 dihedral pdb=" CA ASN R 47 " pdb=" C ASN R 47 " pdb=" N LEU R 48 " pdb=" CA LEU R 48 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 12404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 3372 0.132 - 0.265: 30 0.265 - 0.397: 1 0.397 - 0.529: 0 0.529 - 0.662: 1 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA SER T 101 " pdb=" N SER T 101 " pdb=" C SER T 101 " pdb=" CB SER T 101 " both_signs ideal model delta sigma weight residual False 2.51 3.17 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA PRO N 852 " pdb=" N PRO N 852 " pdb=" C PRO N 852 " pdb=" CB PRO N 852 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA PRO N 137 " pdb=" N PRO N 137 " pdb=" C PRO N 137 " pdb=" CB PRO N 137 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 3401 not shown) Planarity restraints: 3678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY T 100 " -0.063 2.00e-02 2.50e+03 9.37e-02 8.77e+01 pdb=" C GLY T 100 " 0.161 2.00e-02 2.50e+03 pdb=" O GLY T 100 " -0.036 2.00e-02 2.50e+03 pdb=" N SER T 101 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 256 " 0.082 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO N 257 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO N 257 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO N 257 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL N 193 " -0.088 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO N 194 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO N 194 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO N 194 " -0.062 5.00e-02 4.00e+02 ... (remaining 3675 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 21 2.21 - 2.88: 7915 2.88 - 3.56: 31944 3.56 - 4.23: 45274 4.23 - 4.90: 72783 Nonbonded interactions: 157937 Sorted by model distance: nonbonded pdb=" O PHE T 30 " pdb=" O GLY T 100 " model vdw 1.541 3.040 nonbonded pdb=" O PRO N 194 " pdb=" OD1 ASN N 195 " model vdw 1.903 3.040 nonbonded pdb=" O SER Q 167 " pdb=" OG1 THR Q 170 " model vdw 2.120 3.040 nonbonded pdb=" O TRP Q 444 " pdb=" NH1 ARG Q 448 " model vdw 2.136 3.120 nonbonded pdb=" O CYS N 475 " pdb=" OG1 THR N 478 " model vdw 2.152 3.040 ... (remaining 157932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'J' and resid 11 through 342) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.710 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.310 20570 Z= 0.437 Angle : 1.188 27.377 28082 Z= 0.823 Chirality : 0.048 0.662 3404 Planarity : 0.005 0.127 3677 Dihedral : 8.616 81.954 6666 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 3.45 % Allowed : 8.34 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.16), residues: 2495 helix: -2.00 (0.10), residues: 1175 sheet: -3.33 (0.26), residues: 272 loop : 0.09 (0.23), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 166 TYR 0.021 0.002 TYR R 39 PHE 0.025 0.002 PHE H 50 TRP 0.038 0.002 TRP N 362 HIS 0.007 0.001 HIS N 364 Details of bonding type rmsd covalent geometry : bond 0.00651 (20569) covalent geometry : angle 1.18797 (28079) hydrogen bonds : bond 0.14878 ( 1173) hydrogen bonds : angle 9.08948 ( 3423) link_TRANS : bond 0.00059 ( 1) link_TRANS : angle 0.15810 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 349 THR cc_start: 0.8560 (p) cc_final: 0.8207 (t) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1809 time to fit residues: 62.7364 Evaluate side-chains 112 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 355 HIS ** N 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 GLN N 403 HIS ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 HIS F 49 ASN F 112 ASN H 18 HIS H 47 HIS H 62 ASN H 63 ASN ** Q 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN R 163 GLN T 22 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 184 GLN K 75 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.052534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.039357 restraints weight = 262254.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.040326 restraints weight = 197554.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.040259 restraints weight = 145676.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.040447 restraints weight = 134396.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.040698 restraints weight = 121523.041| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2512 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= 0.184 Angle : 0.743 11.920 28082 Z= 0.397 Chirality : 0.041 0.209 3404 Planarity : 0.005 0.085 3677 Dihedral : 5.760 30.589 3025 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.22 % Favored : 90.94 % Rotamer: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.17), residues: 2495 helix: -0.27 (0.13), residues: 1211 sheet: -2.96 (0.25), residues: 284 loop : -0.99 (0.22), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 17 TYR 0.022 0.002 TYR Q 104 PHE 0.025 0.002 PHE F 136 TRP 0.018 0.002 TRP T 90 HIS 0.009 0.002 HIS N 545 Details of bonding type rmsd covalent geometry : bond 0.00381 (20569) covalent geometry : angle 0.74328 (28079) hydrogen bonds : bond 0.04179 ( 1173) hydrogen bonds : angle 6.01622 ( 3423) link_TRANS : bond 0.00157 ( 1) link_TRANS : angle 0.40752 ( 3) *********************** 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 160 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.814 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: N 380 GLN cc_start: 0.9093 (mt0) cc_final: 0.8774 (tt0) REVERT: F 65 ASP cc_start: 0.8843 (t0) cc_final: 0.8433 (m-30) REVERT: Q 308 MET cc_start: 0.8954 (mtp) cc_final: 0.8631 (mtp) REVERT: Q 381 LEU cc_start: 0.9489 (tt) cc_final: 0.9240 (mt) REVERT: Q 485 MET cc_start: 0.8657 (tmm) cc_final: 0.8309 (tmm) REVERT: R 80 MET cc_start: 0.8873 (tpp) cc_final: 0.8509 (tpp) REVERT: V 34 ASP cc_start: 0.9417 (m-30) cc_final: 0.9088 (m-30) outliers start: 2 outliers final: 1 residues processed: 160 average time/residue: 0.1757 time to fit residues: 41.5704 Evaluate side-chains 108 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 27 optimal weight: 0.0470 chunk 160 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 79 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 264 optimal weight: 50.0000 chunk 282 optimal weight: 40.0000 chunk 272 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 243 HIS N 273 GLN ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 418 HIS F 69 GLN F 152 GLN F 204 GLN H 58 HIS H 62 ASN H 63 ASN Q 302 GLN Q 319 GLN Q 377 GLN Q 447 GLN R 65 HIS R 178 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.052320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.039132 restraints weight = 261782.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.039929 restraints weight = 202958.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.040025 restraints weight = 165675.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.040436 restraints weight = 136255.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.040497 restraints weight = 120871.997| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20570 Z= 0.147 Angle : 0.653 12.302 28082 Z= 0.348 Chirality : 0.039 0.214 3404 Planarity : 0.004 0.081 3677 Dihedral : 5.233 31.212 3025 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.78 % Favored : 90.34 % Rotamer: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2495 helix: 0.33 (0.14), residues: 1227 sheet: -2.96 (0.25), residues: 277 loop : -1.29 (0.22), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 166 TYR 0.025 0.002 TYR Q 104 PHE 0.017 0.002 PHE H 50 TRP 0.016 0.001 TRP F 21 HIS 0.007 0.001 HIS V 59 Details of bonding type rmsd covalent geometry : bond 0.00296 (20569) covalent geometry : angle 0.65334 (28079) hydrogen bonds : bond 0.03631 ( 1173) hydrogen bonds : angle 5.35237 ( 3423) link_TRANS : bond 0.00147 ( 1) link_TRANS : angle 0.36590 ( 3) *********************** 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 139 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.865 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: N 335 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8658 (tp-100) REVERT: N 380 GLN cc_start: 0.9176 (mt0) cc_final: 0.8814 (tt0) REVERT: Q 246 MET cc_start: 0.8251 (tpt) cc_final: 0.8034 (tpp) REVERT: Q 308 MET cc_start: 0.9073 (mtp) cc_final: 0.8779 (mtp) REVERT: Q 485 MET cc_start: 0.8784 (tmm) cc_final: 0.8329 (tmm) REVERT: V 34 ASP cc_start: 0.9340 (m-30) cc_final: 0.9085 (m-30) REVERT: V 47 TYR cc_start: 0.9299 (m-80) cc_final: 0.8406 (m-80) REVERT: V 90 PHE cc_start: 0.7422 (p90) cc_final: 0.7171 (p90) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1539 time to fit residues: 32.4909 Evaluate side-chains 104 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 183 optimal weight: 3.9990 chunk 282 optimal weight: 40.0000 chunk 33 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 101 optimal weight: 0.3980 chunk 258 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 31 optimal weight: 0.0040 chunk 63 optimal weight: 0.9980 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN Q 518 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.051822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.038852 restraints weight = 264262.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.039713 restraints weight = 207700.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.039752 restraints weight = 158258.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.040030 restraints weight = 141338.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.040264 restraints weight = 121645.919| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20570 Z= 0.146 Angle : 0.628 12.038 28082 Z= 0.332 Chirality : 0.038 0.179 3404 Planarity : 0.004 0.074 3677 Dihedral : 5.045 27.368 3025 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.49 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.17), residues: 2495 helix: 0.78 (0.15), residues: 1224 sheet: -2.66 (0.26), residues: 291 loop : -1.41 (0.22), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 27 TYR 0.025 0.002 TYR R 39 PHE 0.017 0.001 PHE N 340 TRP 0.023 0.001 TRP F 21 HIS 0.010 0.001 HIS R 172 Details of bonding type rmsd covalent geometry : bond 0.00301 (20569) covalent geometry : angle 0.62783 (28079) hydrogen bonds : bond 0.03366 ( 1173) hydrogen bonds : angle 4.95499 ( 3423) link_TRANS : bond 0.00158 ( 1) link_TRANS : angle 0.35171 ( 3) *********************** 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 133 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.800 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: N 335 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8657 (tp-100) REVERT: N 380 GLN cc_start: 0.9353 (mt0) cc_final: 0.8957 (tt0) REVERT: Q 308 MET cc_start: 0.8999 (mtp) cc_final: 0.8625 (mtp) REVERT: Q 485 MET cc_start: 0.8817 (tmm) cc_final: 0.8399 (tmm) REVERT: V 32 PHE cc_start: 0.9585 (t80) cc_final: 0.9308 (t80) REVERT: V 34 ASP cc_start: 0.9309 (m-30) cc_final: 0.9068 (m-30) REVERT: V 47 TYR cc_start: 0.9332 (m-80) cc_final: 0.8437 (m-80) REVERT: V 72 ASP cc_start: 0.8739 (m-30) cc_final: 0.8518 (m-30) REVERT: V 90 PHE cc_start: 0.7400 (p90) cc_final: 0.7165 (p90) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1607 time to fit residues: 32.4068 Evaluate side-chains 102 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 170 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 267 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 219 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 259 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS H 58 HIS H 63 ASN H 67 HIS ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.051600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.038620 restraints weight = 260839.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.039769 restraints weight = 203009.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.039576 restraints weight = 148119.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.039874 restraints weight = 131627.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.039932 restraints weight = 116459.852| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20570 Z= 0.135 Angle : 0.608 12.058 28082 Z= 0.322 Chirality : 0.038 0.168 3404 Planarity : 0.004 0.076 3677 Dihedral : 4.831 25.952 3025 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.14 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 2495 helix: 1.06 (0.15), residues: 1228 sheet: -2.57 (0.26), residues: 301 loop : -1.51 (0.22), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 31 TYR 0.024 0.001 TYR K 57 PHE 0.016 0.001 PHE N 340 TRP 0.024 0.001 TRP F 21 HIS 0.006 0.001 HIS V 59 Details of bonding type rmsd covalent geometry : bond 0.00278 (20569) covalent geometry : angle 0.60835 (28079) hydrogen bonds : bond 0.03180 ( 1173) hydrogen bonds : angle 4.71110 ( 3423) link_TRANS : bond 0.00148 ( 1) link_TRANS : angle 0.32616 ( 3) *********************** 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 126 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 335 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8709 (tp-100) REVERT: N 380 GLN cc_start: 0.9362 (mt0) cc_final: 0.8978 (tt0) REVERT: F 25 MET cc_start: 0.7813 (pmm) cc_final: 0.7606 (pmm) REVERT: H 145 MET cc_start: 0.9480 (ppp) cc_final: 0.9271 (ppp) REVERT: Q 485 MET cc_start: 0.8774 (tmm) cc_final: 0.8309 (tmm) REVERT: R 116 MET cc_start: 0.9533 (mmp) cc_final: 0.9315 (mmm) REVERT: V 32 PHE cc_start: 0.9540 (t80) cc_final: 0.9081 (t80) REVERT: V 47 TYR cc_start: 0.9335 (m-80) cc_final: 0.8355 (m-80) REVERT: V 72 ASP cc_start: 0.8773 (m-30) cc_final: 0.8564 (m-30) REVERT: V 90 PHE cc_start: 0.7350 (p90) cc_final: 0.7128 (p90) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1582 time to fit residues: 30.2615 Evaluate side-chains 96 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 157 optimal weight: 0.5980 chunk 280 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 222 optimal weight: 40.0000 chunk 235 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 229 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 231 optimal weight: 50.0000 chunk 216 optimal weight: 30.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 267 HIS ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 GLN N 405 ASN H 56 GLN H 63 ASN Q 312 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.050246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.037527 restraints weight = 263553.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.038333 restraints weight = 207712.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.038463 restraints weight = 157681.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.038709 restraints weight = 144095.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.038810 restraints weight = 121094.406| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20570 Z= 0.175 Angle : 0.645 12.028 28082 Z= 0.339 Chirality : 0.039 0.176 3404 Planarity : 0.004 0.078 3677 Dihedral : 4.861 25.131 3025 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.10 % Favored : 91.34 % Rotamer: Outliers : 0.06 % Allowed : 1.27 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.18), residues: 2495 helix: 1.21 (0.15), residues: 1229 sheet: -2.56 (0.26), residues: 312 loop : -1.62 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 29 TYR 0.021 0.002 TYR R 118 PHE 0.018 0.002 PHE N 340 TRP 0.027 0.002 TRP N 527 HIS 0.007 0.001 HIS T 33 Details of bonding type rmsd covalent geometry : bond 0.00363 (20569) covalent geometry : angle 0.64493 (28079) hydrogen bonds : bond 0.03304 ( 1173) hydrogen bonds : angle 4.61207 ( 3423) link_TRANS : bond 0.00186 ( 1) link_TRANS : angle 0.32334 ( 3) *********************** 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 123 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.595 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: F 111 CYS cc_start: 0.9063 (t) cc_final: 0.8823 (t) REVERT: H 145 MET cc_start: 0.9477 (ppp) cc_final: 0.9277 (ppp) REVERT: Q 246 MET cc_start: 0.8364 (tpt) cc_final: 0.8111 (tpt) REVERT: Q 485 MET cc_start: 0.8786 (tmm) cc_final: 0.8394 (tmm) REVERT: R 80 MET cc_start: 0.8682 (tpt) cc_final: 0.8328 (tpt) REVERT: V 32 PHE cc_start: 0.9551 (t80) cc_final: 0.9139 (t80) REVERT: V 47 TYR cc_start: 0.9314 (m-80) cc_final: 0.8384 (m-80) REVERT: V 72 ASP cc_start: 0.8692 (m-30) cc_final: 0.8480 (m-30) REVERT: V 90 PHE cc_start: 0.7496 (p90) cc_final: 0.7295 (p90) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1768 time to fit residues: 32.3308 Evaluate side-chains 89 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 30.0000 chunk 238 optimal weight: 0.4980 chunk 254 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 77 optimal weight: 0.0170 chunk 150 optimal weight: 2.9990 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 HIS F 162 ASN H 63 ASN Q 220 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.050482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.037751 restraints weight = 264440.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.038411 restraints weight = 200421.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.038602 restraints weight = 161967.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.039006 restraints weight = 134492.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.039050 restraints weight = 118631.038| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20570 Z= 0.133 Angle : 0.600 12.139 28082 Z= 0.317 Chirality : 0.038 0.160 3404 Planarity : 0.004 0.079 3677 Dihedral : 4.693 27.407 3025 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.30 % Favored : 91.06 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2495 helix: 1.37 (0.15), residues: 1236 sheet: -2.35 (0.27), residues: 303 loop : -1.70 (0.22), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 31 TYR 0.019 0.001 TYR F 134 PHE 0.015 0.001 PHE N 340 TRP 0.029 0.002 TRP N 527 HIS 0.004 0.001 HIS N 267 Details of bonding type rmsd covalent geometry : bond 0.00272 (20569) covalent geometry : angle 0.60028 (28079) hydrogen bonds : bond 0.03125 ( 1173) hydrogen bonds : angle 4.43741 ( 3423) link_TRANS : bond 0.00173 ( 1) link_TRANS : angle 0.32033 ( 3) *********************** 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 119 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.775 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: F 111 CYS cc_start: 0.9126 (t) cc_final: 0.8882 (t) REVERT: Q 246 MET cc_start: 0.8499 (tpt) cc_final: 0.8246 (tpt) REVERT: Q 485 MET cc_start: 0.8773 (tmm) cc_final: 0.8287 (tmm) REVERT: V 31 ARG cc_start: 0.8568 (mmm160) cc_final: 0.7954 (mmm160) REVERT: V 47 TYR cc_start: 0.9286 (m-80) cc_final: 0.8326 (m-80) REVERT: V 72 ASP cc_start: 0.8743 (m-30) cc_final: 0.8511 (m-30) REVERT: V 90 PHE cc_start: 0.7426 (p90) cc_final: 0.7224 (p90) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1601 time to fit residues: 28.6966 Evaluate side-chains 92 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 221 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 262 optimal weight: 50.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 153 GLN ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN R 100 ASN T 32 GLN ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.050487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.037888 restraints weight = 263002.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.038448 restraints weight = 206709.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.039192 restraints weight = 163714.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.039148 restraints weight = 145795.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.039168 restraints weight = 126572.399| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20570 Z= 0.126 Angle : 0.600 12.073 28082 Z= 0.316 Chirality : 0.038 0.260 3404 Planarity : 0.004 0.074 3677 Dihedral : 4.602 27.692 3025 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.82 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.18), residues: 2495 helix: 1.47 (0.15), residues: 1239 sheet: -2.15 (0.27), residues: 304 loop : -1.74 (0.22), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 31 TYR 0.025 0.001 TYR N 309 PHE 0.023 0.001 PHE F 136 TRP 0.031 0.002 TRP N 527 HIS 0.015 0.001 HIS N 326 Details of bonding type rmsd covalent geometry : bond 0.00257 (20569) covalent geometry : angle 0.59973 (28079) hydrogen bonds : bond 0.03001 ( 1173) hydrogen bonds : angle 4.28968 ( 3423) link_TRANS : bond 0.00179 ( 1) link_TRANS : angle 0.33198 ( 3) *********************** 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 119 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.813 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: F 111 CYS cc_start: 0.9267 (t) cc_final: 0.9024 (t) REVERT: Q 485 MET cc_start: 0.8797 (tmm) cc_final: 0.8282 (tmm) REVERT: V 31 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8058 (mmm160) REVERT: V 47 TYR cc_start: 0.9262 (m-80) cc_final: 0.8230 (m-80) REVERT: V 72 ASP cc_start: 0.8773 (m-30) cc_final: 0.8540 (m-30) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1699 time to fit residues: 30.4351 Evaluate side-chains 89 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 157 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 31 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 207 optimal weight: 40.0000 chunk 143 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN R 75 ASN ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.050824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.038070 restraints weight = 261303.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.039071 restraints weight = 206269.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.038897 restraints weight = 152710.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.039177 restraints weight = 139119.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.039249 restraints weight = 124679.585| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20570 Z= 0.118 Angle : 0.597 12.160 28082 Z= 0.313 Chirality : 0.038 0.276 3404 Planarity : 0.004 0.084 3677 Dihedral : 4.537 26.730 3025 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.82 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.18), residues: 2495 helix: 1.55 (0.15), residues: 1236 sheet: -2.17 (0.28), residues: 293 loop : -1.74 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG Q 406 TYR 0.021 0.001 TYR K 57 PHE 0.010 0.001 PHE N 340 TRP 0.034 0.002 TRP N 527 HIS 0.005 0.001 HIS N 326 Details of bonding type rmsd covalent geometry : bond 0.00237 (20569) covalent geometry : angle 0.59658 (28079) hydrogen bonds : bond 0.02957 ( 1173) hydrogen bonds : angle 4.18340 ( 3423) link_TRANS : bond 0.00166 ( 1) link_TRANS : angle 0.32582 ( 3) *********************** 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 120 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 377 MET cc_start: 0.5262 (mtt) cc_final: 0.5018 (mtt) REVERT: F 111 CYS cc_start: 0.9372 (t) cc_final: 0.9170 (t) REVERT: Q 113 MET cc_start: 0.9402 (mtm) cc_final: 0.9012 (ptp) REVERT: Q 246 MET cc_start: 0.8537 (tpt) cc_final: 0.8312 (tpp) REVERT: Q 485 MET cc_start: 0.8813 (tmm) cc_final: 0.8289 (tmm) REVERT: R 80 MET cc_start: 0.8801 (tpt) cc_final: 0.8286 (mpp) REVERT: V 31 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8399 (mmm160) REVERT: V 47 TYR cc_start: 0.9252 (m-80) cc_final: 0.8188 (m-80) REVERT: V 72 ASP cc_start: 0.8883 (m-30) cc_final: 0.8645 (m-30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1718 time to fit residues: 31.1607 Evaluate side-chains 91 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 56 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.050697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.037947 restraints weight = 262404.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.039097 restraints weight = 205165.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.038881 restraints weight = 149709.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.039125 restraints weight = 136562.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.039171 restraints weight = 120462.645| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20570 Z= 0.119 Angle : 0.604 12.132 28082 Z= 0.315 Chirality : 0.038 0.318 3404 Planarity : 0.004 0.065 3677 Dihedral : 4.465 26.655 3025 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.29 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.18), residues: 2495 helix: 1.57 (0.15), residues: 1250 sheet: -2.10 (0.28), residues: 292 loop : -1.78 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 27 TYR 0.019 0.001 TYR K 57 PHE 0.024 0.001 PHE F 136 TRP 0.034 0.002 TRP N 527 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00240 (20569) covalent geometry : angle 0.60376 (28079) hydrogen bonds : bond 0.02912 ( 1173) hydrogen bonds : angle 4.11118 ( 3423) link_TRANS : bond 0.00166 ( 1) link_TRANS : angle 0.34601 ( 3) ********************** 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 121 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.491 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: F 88 LEU cc_start: 0.9685 (tp) cc_final: 0.9467 (mm) REVERT: F 111 CYS cc_start: 0.9333 (t) cc_final: 0.9042 (t) REVERT: F 117 MET cc_start: 0.7973 (mtt) cc_final: 0.7729 (mtt) REVERT: Q 113 MET cc_start: 0.9345 (mtm) cc_final: 0.8887 (ptp) REVERT: Q 246 MET cc_start: 0.8524 (tpt) cc_final: 0.8322 (tpp) REVERT: Q 485 MET cc_start: 0.8739 (tmm) cc_final: 0.8305 (tmm) REVERT: R 80 MET cc_start: 0.8775 (tpt) cc_final: 0.8296 (mpp) REVERT: R 175 ASP cc_start: 0.9321 (p0) cc_final: 0.9113 (p0) REVERT: V 47 TYR cc_start: 0.9208 (m-80) cc_final: 0.8134 (m-80) REVERT: V 72 ASP cc_start: 0.8812 (m-30) cc_final: 0.8556 (m-30) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1437 time to fit residues: 26.5046 Evaluate side-chains 91 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 260 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 159 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 237 optimal weight: 50.0000 chunk 92 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** Q 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.049277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.036753 restraints weight = 270024.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.037602 restraints weight = 213187.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.037539 restraints weight = 159021.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.037773 restraints weight = 146549.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.037792 restraints weight = 128131.579| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20570 Z= 0.187 Angle : 0.654 11.956 28082 Z= 0.345 Chirality : 0.039 0.278 3404 Planarity : 0.004 0.069 3677 Dihedral : 4.631 32.041 3025 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.14 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2495 helix: 1.53 (0.15), residues: 1253 sheet: -1.95 (0.28), residues: 303 loop : -1.90 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG H 19 TYR 0.025 0.002 TYR K 57 PHE 0.017 0.002 PHE R 112 TRP 0.032 0.002 TRP N 527 HIS 0.008 0.001 HIS T 33 Details of bonding type rmsd covalent geometry : bond 0.00390 (20569) covalent geometry : angle 0.65415 (28079) hydrogen bonds : bond 0.03194 ( 1173) hydrogen bonds : angle 4.24297 ( 3423) link_TRANS : bond 0.00215 ( 1) link_TRANS : angle 0.34758 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3246.74 seconds wall clock time: 56 minutes 59.57 seconds (3419.57 seconds total)