Starting phenix.real_space_refine on Mon Mar 18 07:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/03_2024/5u0p_8479.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/03_2024/5u0p_8479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/03_2024/5u0p_8479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/03_2024/5u0p_8479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/03_2024/5u0p_8479.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0p_8479/03_2024/5u0p_8479.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 12745 2.51 5 N 3601 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R ARG 206": "NH1" <-> "NH2" Residue "T PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20268 Number of models: 1 Model: "" Number of chains: 16 Chain: "N" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3887 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'CIS': 19, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 478} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'UNK:plan-1': 22, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "F" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1590 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1493 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Chain: "Q" Number of atoms: 3831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3831 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 485} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 164 Chain: "R" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1694 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 11, 'TRANS': 191} Chain: "T" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1455 Classifications: {'peptide': 179} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "K" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 769 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 949 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "G" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 965 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 181} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 667 Unresolved non-hydrogen angles: 838 Unresolved non-hydrogen dihedrals: 562 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 344 Chain: "U" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 608 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 217 Chain: "3" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 96} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 272 Chain: "I" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Chain: "2" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 388 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 73} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "S" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Chain breaks: 6 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "J" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 660 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'TRANS': 131} Chain breaks: 3 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 132 Planarities with less than four sites: {'UNK:plan-1': 132} Unresolved non-hydrogen planarities: 132 Time building chain proxies: 11.26, per 1000 atoms: 0.56 Number of scatterers: 20268 At special positions: 0 Unit cell: (158.51, 255.45, 131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 3867 8.00 N 3601 7.00 C 12745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.96 Conformation dependent library (CDL) restraints added in 3.0 seconds 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5738 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 19 sheets defined 67.4% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'N' and resid 87 through 93 removed outlier: 3.774A pdb=" N LYS N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 119 removed outlier: 3.523A pdb=" N SER N 109 " --> pdb=" O ARG N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 132 removed outlier: 4.128A pdb=" N SER N 130 " --> pdb=" O SER N 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG N 132 " --> pdb=" O GLY N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 172 removed outlier: 5.070A pdb=" N ARG N 166 " --> pdb=" O ASN N 162 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE N 167 " --> pdb=" O MET N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 254 removed outlier: 4.019A pdb=" N ARG N 237 " --> pdb=" O PRO N 233 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU N 241 " --> pdb=" O ARG N 237 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU N 242 " --> pdb=" O VAL N 238 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS N 243 " --> pdb=" O PHE N 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU N 244 " --> pdb=" O ILE N 240 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA N 249 " --> pdb=" O ASN N 245 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE N 252 " --> pdb=" O ILE N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 288 removed outlier: 3.727A pdb=" N TYR N 263 " --> pdb=" O LEU N 259 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE N 265 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE N 269 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS N 270 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN N 281 " --> pdb=" O LEU N 277 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 342 removed outlier: 3.510A pdb=" N ARG N 342 " --> pdb=" O SER N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 378 through 402 removed outlier: 3.733A pdb=" N LEU N 382 " --> pdb=" O ASP N 378 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU N 383 " --> pdb=" O ALA N 379 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 453 Processing helix chain 'N' and resid 453 through 459 Processing helix chain 'N' and resid 465 through 484 removed outlier: 3.793A pdb=" N ILE N 476 " --> pdb=" O TYR N 472 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN N 477 " --> pdb=" O PHE N 473 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU N 482 " --> pdb=" O THR N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 550 through 576 removed outlier: 4.004A pdb=" N LEU N 559 " --> pdb=" O SER N 555 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER N 560 " --> pdb=" O PHE N 556 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU N 563 " --> pdb=" O LEU N 559 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS N 576 " --> pdb=" O VAL N 572 " (cutoff:3.500A) Processing helix chain 'N' and resid 884 through 900 removed outlier: 3.929A pdb=" N UNK N 889 " --> pdb=" O UNK N 885 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N UNK N 890 " --> pdb=" O UNK N 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.872A pdb=" N LEU F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 59 removed outlier: 3.553A pdb=" N MET F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 120 through 142 removed outlier: 3.504A pdb=" N LEU F 124 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 211 removed outlier: 3.827A pdb=" N MET F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 37 removed outlier: 3.509A pdb=" N LYS H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 65 removed outlier: 3.604A pdb=" N ILE H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 74 removed outlier: 3.730A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 95 removed outlier: 3.607A pdb=" N THR H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.941A pdb=" N GLU H 113 " --> pdb=" O ASN H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 151 removed outlier: 3.722A pdb=" N GLN H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 148 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR H 151 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 198 removed outlier: 3.964A pdb=" N ALA H 178 " --> pdb=" O GLU H 174 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR H 179 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 12 Processing helix chain 'Q' and resid 13 through 19 Processing helix chain 'Q' and resid 29 through 39 removed outlier: 4.633A pdb=" N GLN Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 59 removed outlier: 3.934A pdb=" N ASP Q 50 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU Q 54 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 65 removed outlier: 3.949A pdb=" N ILE Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 76 removed outlier: 3.636A pdb=" N GLU Q 75 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 91 removed outlier: 3.846A pdb=" N THR Q 84 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU Q 85 " --> pdb=" O GLU Q 81 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP Q 86 " --> pdb=" O PHE Q 82 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER Q 87 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 95 removed outlier: 4.099A pdb=" N GLU Q 95 " --> pdb=" O ASN Q 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 92 through 95' Processing helix chain 'Q' and resid 102 through 131 removed outlier: 3.818A pdb=" N GLU Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA Q 122 " --> pdb=" O GLU Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 141 removed outlier: 3.594A pdb=" N ILE Q 141 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 147 Processing helix chain 'Q' and resid 165 through 214 removed outlier: 4.129A pdb=" N ALA Q 169 " --> pdb=" O LYS Q 165 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS Q 176 " --> pdb=" O ALA Q 172 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU Q 203 " --> pdb=" O GLU Q 199 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR Q 204 " --> pdb=" O THR Q 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR Q 205 " --> pdb=" O GLU Q 201 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR Q 206 " --> pdb=" O HIS Q 202 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU Q 207 " --> pdb=" O GLU Q 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA Q 214 " --> pdb=" O LYS Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 321 removed outlier: 3.611A pdb=" N LYS Q 296 " --> pdb=" O SER Q 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN Q 319 " --> pdb=" O LEU Q 315 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER Q 320 " --> pdb=" O GLN Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 322 through 325 Processing helix chain 'Q' and resid 377 through 404 removed outlier: 3.672A pdb=" N ALA Q 393 " --> pdb=" O LEU Q 389 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS Q 394 " --> pdb=" O ASN Q 390 " (cutoff:3.500A) Processing helix chain 'Q' and resid 409 through 414 removed outlier: 3.825A pdb=" N LEU Q 413 " --> pdb=" O GLN Q 409 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR Q 414 " --> pdb=" O GLN Q 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 409 through 414' Processing helix chain 'Q' and resid 425 through 447 removed outlier: 3.644A pdb=" N TYR Q 432 " --> pdb=" O LEU Q 428 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 removed outlier: 3.664A pdb=" N LYS Q 462 " --> pdb=" O PRO Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 473 removed outlier: 3.536A pdb=" N ASN Q 471 " --> pdb=" O LEU Q 467 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU Q 473 " --> pdb=" O LEU Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 522 through 543 removed outlier: 3.592A pdb=" N VAL Q 526 " --> pdb=" O SER Q 522 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS Q 533 " --> pdb=" O TYR Q 529 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER Q 538 " --> pdb=" O ILE Q 534 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 24 removed outlier: 3.657A pdb=" N VAL R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS R 24 " --> pdb=" O ASN R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 76 Processing helix chain 'R' and resid 110 through 116 removed outlier: 4.068A pdb=" N GLU R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 197 Processing helix chain 'R' and resid 198 through 200 No H-bonds generated for 'chain 'R' and resid 198 through 200' Processing helix chain 'T' and resid 14 through 22 Proline residue: T 20 - end of helix Processing helix chain 'T' and resid 79 through 87 removed outlier: 3.692A pdb=" N ILE T 83 " --> pdb=" O GLU T 79 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 138 Processing helix chain 'T' and resid 139 through 146 removed outlier: 3.782A pdb=" N PHE T 146 " --> pdb=" O ILE T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 175 through 186 removed outlier: 3.789A pdb=" N LEU T 179 " --> pdb=" O SER T 175 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE T 182 " --> pdb=" O LEU T 178 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS T 183 " --> pdb=" O LEU T 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 189 No H-bonds generated for 'chain 'T' and resid 187 through 189' Processing helix chain 'K' and resid 17 through 29 removed outlier: 4.363A pdb=" N VAL K 21 " --> pdb=" O ASP K 17 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 47 removed outlier: 4.620A pdb=" N ASP K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER K 36 " --> pdb=" O PRO K 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE K 45 " --> pdb=" O CYS K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 82 removed outlier: 3.718A pdb=" N LEU K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 68 " --> pdb=" O THR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 111 Processing helix chain 'V' and resid 6 through 39 removed outlier: 3.801A pdb=" N LEU V 10 " --> pdb=" O PHE V 6 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE V 35 " --> pdb=" O ARG V 31 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU V 36 " --> pdb=" O PHE V 32 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP V 37 " --> pdb=" O GLN V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 83 removed outlier: 4.030A pdb=" N ALA V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Proline residue: V 51 - end of helix removed outlier: 3.770A pdb=" N TYR V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 112 Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.784A pdb=" N UNK D 19 " --> pdb=" O UNK D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 40 Processing helix chain 'D' and resid 40 through 87 removed outlier: 4.029A pdb=" N UNK D 44 " --> pdb=" O UNK D 40 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N UNK D 62 " --> pdb=" O UNK D 58 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N UNK D 63 " --> pdb=" O UNK D 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N UNK D 64 " --> pdb=" O UNK D 60 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK D 81 " --> pdb=" O UNK D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'G' and resid 18 through 23 removed outlier: 3.989A pdb=" N LYS G 21 " --> pdb=" O PRO G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 38 removed outlier: 3.538A pdb=" N ILE G 28 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 31 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.021A pdb=" N PHE G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.899A pdb=" N ASP G 79 " --> pdb=" O GLN G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 222 through 240 removed outlier: 4.119A pdb=" N GLU G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU G 230 " --> pdb=" O ARG G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 245 removed outlier: 3.799A pdb=" N LEU G 244 " --> pdb=" O ASN G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 258 removed outlier: 3.993A pdb=" N SER G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 266 removed outlier: 3.914A pdb=" N ILE G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 316 Proline residue: G 278 - end of helix removed outlier: 3.818A pdb=" N SER G 281 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU G 290 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS G 291 " --> pdb=" O MET G 287 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 293 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN G 299 " --> pdb=" O HIS G 295 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL G 300 " --> pdb=" O GLU G 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG G 304 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THR G 305 " --> pdb=" O GLU G 301 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG G 308 " --> pdb=" O ARG G 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN G 309 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 330 Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'U' and resid 4 through 11 removed outlier: 3.660A pdb=" N LEU U 8 " --> pdb=" O ARG U 4 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN U 9 " --> pdb=" O CYS U 5 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP U 10 " --> pdb=" O THR U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 22 removed outlier: 3.957A pdb=" N THR U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE U 19 " --> pdb=" O VAL U 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR U 20 " --> pdb=" O ALA U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 25 No H-bonds generated for 'chain 'U' and resid 23 through 25' Processing helix chain 'U' and resid 27 through 31 Processing helix chain 'U' and resid 51 through 79 removed outlier: 3.963A pdb=" N GLN U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE U 56 " --> pdb=" O GLU U 52 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL U 66 " --> pdb=" O ALA U 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE U 69 " --> pdb=" O LEU U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 137 removed outlier: 3.646A pdb=" N GLU U 91 " --> pdb=" O LYS U 87 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU U 102 " --> pdb=" O ASN U 98 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU U 105 " --> pdb=" O GLU U 101 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU U 106 " --> pdb=" O GLU U 102 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU U 111 " --> pdb=" O ARG U 107 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER U 112 " --> pdb=" O LYS U 108 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP U 116 " --> pdb=" O SER U 112 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU U 117 " --> pdb=" O GLU U 113 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN U 120 " --> pdb=" O ASP U 116 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS U 133 " --> pdb=" O GLY U 129 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL U 134 " --> pdb=" O ARG U 130 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU U 135 " --> pdb=" O LEU U 131 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 8 Processing helix chain '3' and resid 15 through 25 removed outlier: 4.067A pdb=" N GLU 3 20 " --> pdb=" O ARG 3 16 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU 3 21 " --> pdb=" O PHE 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 29 Processing helix chain '3' and resid 31 through 36 Processing helix chain '3' and resid 45 through 53 removed outlier: 4.023A pdb=" N GLN 3 49 " --> pdb=" O GLU 3 45 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 58 Processing helix chain '3' and resid 67 through 79 removed outlier: 4.429A pdb=" N CYS 3 71 " --> pdb=" O ILE 3 67 " (cutoff:3.500A) Processing helix chain '3' and resid 90 through 92 No H-bonds generated for 'chain '3' and resid 90 through 92' Processing helix chain '3' and resid 93 through 99 removed outlier: 3.892A pdb=" N ASN 3 97 " --> pdb=" O SER 3 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP 3 98 " --> pdb=" O LYS 3 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 58 removed outlier: 4.069A pdb=" N ILE I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG I 54 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 88 removed outlier: 3.827A pdb=" N VAL I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS I 73 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE I 76 " --> pdb=" O GLU I 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE I 77 " --> pdb=" O LYS I 73 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 Processing helix chain 'I' and resid 111 through 114 Processing helix chain 'I' and resid 115 through 121 Processing helix chain '2' and resid 2 through 22 Processing helix chain '2' and resid 32 through 45 Proline residue: 2 42 - end of helix Processing helix chain '2' and resid 62 through 70 Processing helix chain 'S' and resid 72 through 82 Processing helix chain 'S' and resid 252 through 265 Processing helix chain 'S' and resid 272 through 287 removed outlier: 3.580A pdb=" N UNK S 287 " --> pdb=" O UNK S 283 " (cutoff:3.500A) Processing helix chain 'S' and resid 302 through 321 Processing helix chain 'S' and resid 332 through 348 Processing helix chain 'S' and resid 352 through 364 removed outlier: 3.833A pdb=" N UNK S 356 " --> pdb=" O UNK S 352 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N UNK S 357 " --> pdb=" O UNK S 353 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK S 362 " --> pdb=" O UNK S 358 " (cutoff:3.500A) Processing helix chain 'S' and resid 382 through 399 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 20 through 22 No H-bonds generated for 'chain 'J' and resid 20 through 22' Processing helix chain 'J' and resid 26 through 55 removed outlier: 3.706A pdb=" N UNK J 31 " --> pdb=" O UNK J 27 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK J 34 " --> pdb=" O UNK J 30 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N UNK J 40 " --> pdb=" O UNK J 36 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N UNK J 43 " --> pdb=" O UNK J 39 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N UNK J 44 " --> pdb=" O UNK J 40 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N UNK J 52 " --> pdb=" O UNK J 48 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N UNK J 53 " --> pdb=" O UNK J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 204 Processing helix chain 'J' and resid 311 through 341 removed outlier: 3.801A pdb=" N UNK J 330 " --> pdb=" O UNK J 326 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N UNK J 335 " --> pdb=" O UNK J 331 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N UNK J 338 " --> pdb=" O UNK J 334 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK J 339 " --> pdb=" O UNK J 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 187 through 190 removed outlier: 6.814A pdb=" N SER N 198 " --> pdb=" O VAL N 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 307 through 308 Processing sheet with id=AA3, first strand: chain 'N' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'N' and resid 415 through 416 removed outlier: 3.733A pdb=" N LEU N 415 " --> pdb=" O ASN N 422 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU N 423 " --> pdb=" O VAL N 436 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE N 425 " --> pdb=" O ARG N 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 520 through 522 removed outlier: 3.696A pdb=" N SER N 528 " --> pdb=" O ASN N 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 76 through 79 removed outlier: 6.861A pdb=" N ILE F 91 " --> pdb=" O VAL F 107 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL F 107 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS F 93 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE F 109 " --> pdb=" O TYR F 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR F 116 " --> pdb=" O PHE F 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 148 through 150 Processing sheet with id=AA8, first strand: chain 'Q' and resid 218 through 220 removed outlier: 6.184A pdb=" N LEU Q 227 " --> pdb=" O ILE Q 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 277 through 281 removed outlier: 6.368A pdb=" N ILE Q 270 " --> pdb=" O ILE Q 278 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER Q 280 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE Q 268 " --> pdb=" O SER Q 280 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 327 through 328 Processing sheet with id=AB2, first strand: chain 'Q' and resid 454 through 455 removed outlier: 3.724A pdb=" N SER Q 481 " --> pdb=" O MET Q 455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id=AB4, first strand: chain 'R' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'R' and resid 8 through 10 removed outlier: 3.799A pdb=" N LEU R 129 " --> pdb=" O ILE R 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 8 through 10 removed outlier: 3.799A pdb=" N LEU R 129 " --> pdb=" O ILE R 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 102 through 104 removed outlier: 3.919A pdb=" N LEU R 104 " --> pdb=" O TRP R 78 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TRP R 78 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU R 56 " --> pdb=" O TYR R 39 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR R 39 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'T' and resid 57 through 58 removed outlier: 3.788A pdb=" N LYS T 57 " --> pdb=" O HIS T 33 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS T 33 " --> pdb=" O LYS T 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 113 through 114 1188 hydrogen bonds defined for protein. 3423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.37 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6831 1.33 - 1.45: 2525 1.45 - 1.57: 11128 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 20570 Sorted by residual: bond pdb=" C GLY T 100 " pdb=" O GLY T 100 " ideal model delta sigma weight residual 1.235 1.545 -0.310 1.35e-02 5.49e+03 5.28e+02 bond pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 1.332 1.576 -0.244 1.40e-02 5.10e+03 3.03e+02 bond pdb=" N SER T 101 " pdb=" CA SER T 101 " ideal model delta sigma weight residual 1.457 1.545 -0.087 1.29e-02 6.01e+03 4.57e+01 bond pdb=" CA GLY T 100 " pdb=" C GLY T 100 " ideal model delta sigma weight residual 1.514 1.591 -0.077 1.41e-02 5.03e+03 2.98e+01 bond pdb=" N PRO N 194 " pdb=" CD PRO N 194 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 20565 not shown) Histogram of bond angle deviations from ideal: 96.97 - 106.39: 469 106.39 - 115.81: 13225 115.81 - 125.23: 14124 125.23 - 134.65: 260 134.65 - 144.07: 4 Bond angle restraints: 28082 Sorted by residual: angle pdb=" O GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 122.70 102.99 19.71 1.30e+00 5.92e-01 2.30e+02 angle pdb=" CA GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " ideal model delta sigma weight residual 116.69 144.07 -27.38 2.04e+00 2.40e-01 1.80e+02 angle pdb=" C LYS N 301 " pdb=" N PRO N 302 " pdb=" CA PRO N 302 " ideal model delta sigma weight residual 120.38 107.99 12.39 1.03e+00 9.43e-01 1.45e+02 angle pdb=" C LYS R 153 " pdb=" N PRO R 154 " pdb=" CA PRO R 154 " ideal model delta sigma weight residual 119.66 126.31 -6.65 7.20e-01 1.93e+00 8.53e+01 angle pdb=" CA PRO N 194 " pdb=" N PRO N 194 " pdb=" CD PRO N 194 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.25e+01 ... (remaining 28077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 12100 16.39 - 32.78: 231 32.78 - 49.17: 54 49.17 - 65.56: 7 65.56 - 81.95: 13 Dihedral angle restraints: 12405 sinusoidal: 3718 harmonic: 8687 Sorted by residual: dihedral pdb=" CA GLY T 100 " pdb=" C GLY T 100 " pdb=" N SER T 101 " pdb=" CA SER T 101 " ideal model delta harmonic sigma weight residual -180.00 -139.33 -40.67 0 5.00e+00 4.00e-02 6.62e+01 dihedral pdb=" N SER T 101 " pdb=" C SER T 101 " pdb=" CA SER T 101 " pdb=" CB SER T 101 " ideal model delta harmonic sigma weight residual 122.80 102.92 19.88 0 2.50e+00 1.60e-01 6.32e+01 dihedral pdb=" CA ASN R 47 " pdb=" C ASN R 47 " pdb=" N LEU R 48 " pdb=" CA LEU R 48 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 12402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 3372 0.132 - 0.265: 30 0.265 - 0.397: 1 0.397 - 0.529: 0 0.529 - 0.662: 1 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA SER T 101 " pdb=" N SER T 101 " pdb=" C SER T 101 " pdb=" CB SER T 101 " both_signs ideal model delta sigma weight residual False 2.51 3.17 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA PRO N 852 " pdb=" N PRO N 852 " pdb=" C PRO N 852 " pdb=" CB PRO N 852 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA PRO N 137 " pdb=" N PRO N 137 " pdb=" C PRO N 137 " pdb=" CB PRO N 137 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 3401 not shown) Planarity restraints: 3678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY T 100 " -0.063 2.00e-02 2.50e+03 9.37e-02 8.77e+01 pdb=" C GLY T 100 " 0.161 2.00e-02 2.50e+03 pdb=" O GLY T 100 " -0.036 2.00e-02 2.50e+03 pdb=" N SER T 101 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 256 " 0.082 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO N 257 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO N 257 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO N 257 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL N 193 " -0.088 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO N 194 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO N 194 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO N 194 " -0.062 5.00e-02 4.00e+02 ... (remaining 3675 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 21 2.21 - 2.88: 7915 2.88 - 3.56: 31944 3.56 - 4.23: 45274 4.23 - 4.90: 72783 Nonbonded interactions: 157937 Sorted by model distance: nonbonded pdb=" O PHE T 30 " pdb=" O GLY T 100 " model vdw 1.541 3.040 nonbonded pdb=" O PRO N 194 " pdb=" OD1 ASN N 195 " model vdw 1.903 3.040 nonbonded pdb=" O SER Q 167 " pdb=" OG1 THR Q 170 " model vdw 2.120 2.440 nonbonded pdb=" O TRP Q 444 " pdb=" NH1 ARG Q 448 " model vdw 2.136 2.520 nonbonded pdb=" O CYS N 475 " pdb=" OG1 THR N 478 " model vdw 2.152 2.440 ... (remaining 157932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'J' and resid 11 through 342) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.010 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.100 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 54.850 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.350 ------------------------------------------------------------------------------- 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= 0.402 Angle : 1.188 27.377 28082 Z= 0.823 Chirality : 0.048 0.662 3404 Planarity : 0.005 0.127 3678 Dihedral : 8.615 81.954 6667 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 3.45 % Allowed : 8.34 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2495 helix: -2.00 (0.10), residues: 1175 sheet: -3.33 (0.26), residues: 272 loop : 0.09 (0.23), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 362 HIS 0.007 0.001 HIS N 364 PHE 0.025 0.002 PHE H 50 TYR 0.021 0.002 TYR R 39 ARG 0.013 0.001 ARG N 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4990 Ramachandran restraints generated. 2495 Oldfield, 0 Emsley, 2495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 349 THR cc_start: 0.8560 (p) cc_final: 0.8206 (t) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.4080 time to fit residues: 139.6637 Evaluate side-chains 112 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 7.9990 chunk 216 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 355 HIS N 364 HIS N 380 GLN N 403 HIS ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 HIS F 49 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN H 18 HIS H 25 GLN H 47 HIS H 62 ASN H 63 ASN ** Q 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN Q 518 ASN R 51 GLN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN R 163 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 184 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20570 Z= 0.215 Angle : 0.716 12.000 28082 Z= 0.382 Chirality : 0.040 0.189 3404 Planarity : 0.005 0.086 3678 Dihedral : 5.700 30.736 3026 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.10 % Favored : 90.98 % Rotamer: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2495 helix: -0.35 (0.13), residues: 1214 sheet: -2.94 (0.25), residues: 283 loop : -1.01 (0.22), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 362 HIS 0.009 0.002 HIS H 47 PHE 0.026 0.002 PHE Q 454 TYR 0.034 0.002 TYR Q 104 ARG 0.021 0.001 ARG F 17 *********************** 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 163 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.211 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: Q 308 MET cc_start: 0.8751 (mtp) cc_final: 0.8491 (mtp) REVERT: R 80 MET cc_start: 0.8253 (tpp) cc_final: 0.7845 (tpp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.3574 time to fit residues: 86.5704 Evaluate side-chains 111 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 259 optimal weight: 10.0000 chunk 280 optimal weight: 50.0000 chunk 230 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 243 HIS N 273 GLN ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 405 ASN ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 469 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 67 HIS Q 302 GLN Q 377 GLN Q 447 GLN Q 525 ASN ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN R 160 ASN R 178 ASN T 22 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3194 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= 0.227 Angle : 0.670 15.873 28082 Z= 0.356 Chirality : 0.039 0.203 3404 Planarity : 0.004 0.081 3678 Dihedral : 5.222 31.134 3026 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.66 % Favored : 90.46 % Rotamer: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2495 helix: 0.45 (0.14), residues: 1230 sheet: -2.92 (0.25), residues: 299 loop : -1.35 (0.22), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 21 HIS 0.004 0.001 HIS T 33 PHE 0.019 0.002 PHE N 340 TYR 0.041 0.002 TYR Q 104 ARG 0.007 0.001 ARG N 274 *********************** 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 130 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.854 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: Q 308 MET cc_start: 0.8801 (mtp) cc_final: 0.8568 (mtp) REVERT: R 80 MET cc_start: 0.8435 (tpp) cc_final: 0.7982 (tpp) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.3407 time to fit residues: 66.6935 Evaluate side-chains 86 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.0270 chunk 194 optimal weight: 0.2980 chunk 134 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 174 optimal weight: 8.9990 chunk 260 optimal weight: 40.0000 chunk 275 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 246 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 204 GLN H 58 HIS H 62 ASN H 63 ASN Q 319 GLN Q 447 GLN Q 525 ASN R 65 HIS ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20570 Z= 0.157 Angle : 0.612 12.024 28082 Z= 0.323 Chirality : 0.038 0.185 3404 Planarity : 0.004 0.073 3678 Dihedral : 4.985 28.020 3026 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.74 % Favored : 91.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2495 helix: 0.81 (0.15), residues: 1237 sheet: -2.73 (0.24), residues: 306 loop : -1.45 (0.22), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 21 HIS 0.004 0.001 HIS N 159 PHE 0.022 0.001 PHE F 136 TYR 0.033 0.001 TYR Q 104 ARG 0.006 0.000 ARG N 434 *********************** 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 137 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.201 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 434 ARG cc_start: 0.7368 (ttp80) cc_final: 0.7046 (ttp80) REVERT: F 203 MET cc_start: 0.8785 (mmm) cc_final: 0.8567 (mmp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3624 time to fit residues: 74.0591 Evaluate side-chains 97 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 205 optimal weight: 0.9990 chunk 113 optimal weight: 0.0050 chunk 235 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 140 optimal weight: 2.9990 chunk 247 optimal weight: 0.0870 chunk 69 optimal weight: 4.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 418 HIS ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 447 GLN Q 525 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20570 Z= 0.170 Angle : 0.599 11.898 28082 Z= 0.317 Chirality : 0.037 0.169 3404 Planarity : 0.004 0.075 3678 Dihedral : 4.803 34.959 3026 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.30 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2495 helix: 1.17 (0.15), residues: 1232 sheet: -2.61 (0.26), residues: 291 loop : -1.49 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP N 527 HIS 0.003 0.001 HIS N 364 PHE 0.016 0.001 PHE H 30 TYR 0.028 0.001 TYR Q 104 ARG 0.003 0.000 ARG F 29 *********************** 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 129 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 434 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7214 (ttp80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3575 time to fit residues: 70.7383 Evaluate side-chains 94 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 267 HIS ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 312 ASN Q 447 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20570 Z= 0.250 Angle : 0.664 11.833 28082 Z= 0.352 Chirality : 0.038 0.186 3404 Planarity : 0.004 0.078 3678 Dihedral : 4.925 28.691 3026 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.34 % Favored : 91.10 % Rotamer: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2495 helix: 1.29 (0.15), residues: 1231 sheet: -2.42 (0.26), residues: 310 loop : -1.63 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 527 HIS 0.018 0.001 HIS N 545 PHE 0.026 0.002 PHE F 136 TYR 0.023 0.002 TYR N 172 ARG 0.008 0.001 ARG T 27 *********************** 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 120 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 434 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7199 (ttp80) REVERT: F 117 MET cc_start: 0.5000 (mmp) cc_final: 0.4680 (mmp) REVERT: V 31 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7431 (mmm160) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.3459 time to fit residues: 63.8537 Evaluate side-chains 85 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 156 optimal weight: 0.0870 chunk 232 optimal weight: 50.0000 chunk 153 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 126 optimal weight: 0.3980 overall best weight: 0.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 447 GLN Q 525 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.4570 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= 0.157 Angle : 0.600 12.041 28082 Z= 0.316 Chirality : 0.038 0.166 3404 Planarity : 0.004 0.077 3678 Dihedral : 4.709 30.451 3026 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.94 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2495 helix: 1.48 (0.15), residues: 1239 sheet: -2.10 (0.27), residues: 296 loop : -1.66 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 527 HIS 0.008 0.001 HIS N 326 PHE 0.019 0.001 PHE R 112 TYR 0.020 0.001 TYR F 134 ARG 0.011 0.000 ARG H 19 *********************** 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 123 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.368 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: N 434 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7336 (ttp80) REVERT: Q 308 MET cc_start: 0.8875 (mtp) cc_final: 0.8558 (mtp) REVERT: V 31 ARG cc_start: 0.7797 (mmm160) cc_final: 0.7405 (mmm160) REVERT: V 32 PHE cc_start: 0.8354 (t80) cc_final: 0.8120 (t80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3329 time to fit residues: 63.1489 Evaluate side-chains 89 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 25 optimal weight: 0.0470 chunk 215 optimal weight: 30.0000 chunk 249 optimal weight: 10.0000 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN H 63 ASN Q 447 GLN R 100 ASN ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20570 Z= 0.155 Angle : 0.596 14.230 28082 Z= 0.312 Chirality : 0.037 0.260 3404 Planarity : 0.004 0.099 3678 Dihedral : 4.609 30.841 3026 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.86 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2495 helix: 1.54 (0.15), residues: 1240 sheet: -2.17 (0.27), residues: 318 loop : -1.67 (0.22), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 527 HIS 0.005 0.001 HIS N 545 PHE 0.025 0.001 PHE F 136 TYR 0.016 0.001 TYR F 134 ARG 0.022 0.001 ARG H 19 *********************** 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 118 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.195 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: N 434 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7339 (ttp80) REVERT: Q 308 MET cc_start: 0.8899 (mtp) cc_final: 0.8678 (mtp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3343 time to fit residues: 61.6177 Evaluate side-chains 85 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 50.0000 chunk 240 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 231 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 270 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 153 GLN N 159 HIS ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS ** N 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 162 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 226 HIS Q 302 GLN Q 447 GLN R 51 GLN R 188 ASN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 20570 Z= 0.425 Angle : 0.880 12.719 28082 Z= 0.465 Chirality : 0.044 0.240 3404 Planarity : 0.006 0.092 3678 Dihedral : 5.566 33.102 3026 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 29.34 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.66 % Favored : 89.70 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.28 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2495 helix: 0.73 (0.14), residues: 1239 sheet: -2.26 (0.28), residues: 291 loop : -2.01 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP T 37 HIS 0.017 0.003 HIS T 33 PHE 0.029 0.003 PHE N 340 TYR 0.032 0.003 TYR N 540 ARG 0.014 0.001 ARG H 19 *********************** 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 98 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 197 PHE cc_start: 0.7205 (t80) cc_final: 0.6989 (t80) REVERT: N 434 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7253 (ttp80) REVERT: F 117 MET cc_start: 0.6267 (mmp) cc_final: 0.5566 (mmp) REVERT: Q 308 MET cc_start: 0.8841 (mtp) cc_final: 0.8635 (mtp) REVERT: Q 485 MET cc_start: 0.8062 (tmm) cc_final: 0.7816 (tmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3169 time to fit residues: 50.4691 Evaluate side-chains 76 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 283 optimal weight: 50.0000 chunk 261 optimal weight: 50.0000 chunk 226 optimal weight: 40.0000 chunk 23 optimal weight: 7.9990 chunk 174 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 240 optimal weight: 0.0770 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 284 GLN N 326 HIS ** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN H 56 GLN H 63 ASN Q 302 GLN Q 447 GLN ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.5582 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= 0.188 Angle : 0.650 12.182 28082 Z= 0.341 Chirality : 0.039 0.335 3404 Planarity : 0.004 0.085 3678 Dihedral : 5.058 29.825 3026 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.94 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2495 helix: 1.38 (0.15), residues: 1250 sheet: -2.01 (0.28), residues: 291 loop : -1.97 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 527 HIS 0.004 0.001 HIS N 329 PHE 0.025 0.001 PHE F 136 TYR 0.026 0.002 TYR F 134 ARG 0.014 0.001 ARG T 27 ********************** 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 108 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 MET cc_start: 0.5315 (mmp) cc_final: 0.4907 (mmm) REVERT: Q 308 MET cc_start: 0.8853 (mtp) cc_final: 0.8583 (mtp) REVERT: V 32 PHE cc_start: 0.8445 (t80) cc_final: 0.8207 (t80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3439 time to fit residues: 59.9995 Evaluate side-chains 77 residues out of total 2373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.0770 chunk 208 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 226 optimal weight: 40.0000 chunk 94 optimal weight: 30.0000 chunk 232 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 198 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 overall best weight: 0.6552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 GLN ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 447 GLN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.049715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.037125 restraints weight = 266482.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.038071 restraints weight = 203489.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.037932 restraints weight = 157388.365| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20570 Z= 0.159 Angle : 0.612 11.944 28082 Z= 0.321 Chirality : 0.038 0.237 3404 Planarity : 0.004 0.078 3678 Dihedral : 4.676 32.877 3026 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.98 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2495 helix: 1.65 (0.15), residues: 1252 sheet: -1.84 (0.28), residues: 298 loop : -1.98 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 527 HIS 0.004 0.001 HIS N 364 PHE 0.012 0.001 PHE R 112 TYR 0.018 0.001 TYR F 134 ARG 0.015 0.001 ARG T 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.10 seconds wall clock time: 58 minutes 18.46 seconds (3498.46 seconds total)