Starting phenix.real_space_refine on Thu Mar 5 09:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xp5_22284/03_2026/6xp5_22284.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xp5_22284/03_2026/6xp5_22284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xp5_22284/03_2026/6xp5_22284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xp5_22284/03_2026/6xp5_22284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xp5_22284/03_2026/6xp5_22284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xp5_22284/03_2026/6xp5_22284.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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 57 5.16 5 C 13216 2.51 5 N 3743 2.21 5 O 4049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21065 Number of models: 1 Model: "" Number of chains: 15 Chain: "U" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1055 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 994 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1202 Classifications: {'peptide': 156} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 836 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain breaks: 3 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "I" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 470 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 10, 'TRANS': 85} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 7, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "N" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4081 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 33, 'TRANS': 510} Chain breaks: 7 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 331 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 5, 'HIS:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 4, 'ARG:plan': 14, 'ASP:plan': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 202 Chain: "Q" Number of atoms: 3571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3571 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 29, 'TRANS': 446} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 6, 'ASN:plan1': 3, 'GLU:plan': 9, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 106 Chain: "Z" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "K" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1255 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 18, 'TRANS': 188} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 8, 'ASP:plan': 11, 'ASN:plan1': 6, 'ARG:plan': 15, 'GLU:plan': 10, 'GLN:plan1': 12, 'HIS:plan': 5, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 299 Chain: "V" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "a" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2941 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 356} Chain breaks: 8 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "b" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1000 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'TRANS': 199} Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 200 Planarities with less than four sites: {'UNK:plan-1': 200} Unresolved non-hydrogen planarities: 200 Time building chain proxies: 4.84, per 1000 atoms: 0.23 Number of scatterers: 21065 At special positions: 0 Unit cell: (189.608, 163.304, 233.448, 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 57 16.00 O 4049 8.00 N 3743 7.00 C 13216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 994.8 milliseconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 17 sheets defined 49.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'U' and resid 3 through 29 removed outlier: 4.008A pdb=" N LEU U 16 " --> pdb=" O MET U 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 removed outlier: 3.987A pdb=" N GLU U 59 " --> pdb=" O SER U 56 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR U 60 " --> pdb=" O PRO U 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 56 through 60' Processing helix chain 'U' and resid 62 through 67 Processing helix chain 'U' and resid 67 through 77 removed outlier: 4.690A pdb=" N VAL U 73 " --> pdb=" O ARG U 69 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS U 74 " --> pdb=" O ASP U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 84 removed outlier: 4.303A pdb=" N LEU U 81 " --> pdb=" O GLN U 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE U 82 " --> pdb=" O ILE U 78 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR U 84 " --> pdb=" O TYR U 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 77 through 84' Processing helix chain 'U' and resid 92 through 134 removed outlier: 3.848A pdb=" N ILE U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU U 101 " --> pdb=" O GLN U 97 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU U 102 " --> pdb=" O LEU U 98 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU U 103 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP U 104 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL U 107 " --> pdb=" O GLU U 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN U 112 " --> pdb=" O THR U 108 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG U 113 " --> pdb=" O ALA U 109 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU U 117 " --> pdb=" O ARG U 113 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU U 124 " --> pdb=" O ARG U 120 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU U 127 " --> pdb=" O VAL U 123 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA U 129 " --> pdb=" O GLY U 125 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU U 130 " --> pdb=" O LYS U 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.867A pdb=" N GLU D 13 " --> pdb=" O PHE D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 72 removed outlier: 5.437A pdb=" N GLU D 42 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 removed outlier: 3.787A pdb=" N SER D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 3.697A pdb=" N LEU D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'F' and resid 35 through 40 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 129 through 132 removed outlier: 3.618A pdb=" N ASN F 132 " --> pdb=" O VAL F 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 129 through 132' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 144 through 154 removed outlier: 4.235A pdb=" N ALA F 151 " --> pdb=" O ARG F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 199 removed outlier: 3.640A pdb=" N LEU F 197 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU F 198 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 removed outlier: 3.925A pdb=" N GLU F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE F 206 " --> pdb=" O MET F 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.910A pdb=" N GLN G 36 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 122 removed outlier: 3.558A pdb=" N ALA G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 139 Processing helix chain 'G' and resid 140 through 157 removed outlier: 4.857A pdb=" N ILE G 150 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS G 151 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR G 152 " --> pdb=" O GLN G 148 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 153 " --> pdb=" O ASP G 149 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE G 157 " --> pdb=" O ILE G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 195 removed outlier: 3.661A pdb=" N ARG G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 195 " --> pdb=" O ALA G 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 66 Proline residue: I 47 - end of helix Proline residue: I 52 - end of helix Processing helix chain 'I' and resid 74 through 104 Proline residue: I 87 - end of helix Proline residue: I 92 - end of helix Processing helix chain 'N' and resid 94 through 107 removed outlier: 4.040A pdb=" N GLU N 98 " --> pdb=" O HIS N 94 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 122 removed outlier: 4.480A pdb=" N HIS N 120 " --> pdb=" O GLY N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 257 removed outlier: 4.001A pdb=" N ARG N 239 " --> pdb=" O GLU N 235 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 312 through 328 removed outlier: 4.231A pdb=" N ALA N 316 " --> pdb=" O GLU N 312 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL N 317 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP N 320 " --> pdb=" O ALA N 316 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU N 323 " --> pdb=" O TYR N 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 351 Processing helix chain 'N' and resid 352 through 359 Processing helix chain 'N' and resid 360 through 362 No H-bonds generated for 'chain 'N' and resid 360 through 362' Processing helix chain 'N' and resid 443 through 462 Processing helix chain 'N' and resid 537 through 557 removed outlier: 4.166A pdb=" N GLU N 541 " --> pdb=" O SER N 537 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA N 554 " --> pdb=" O SER N 550 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN N 555 " --> pdb=" O VAL N 551 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY N 556 " --> pdb=" O LEU N 552 " (cutoff:3.500A) Processing helix chain 'N' and resid 574 through 578 removed outlier: 3.701A pdb=" N VAL N 577 " --> pdb=" O ARG N 574 " (cutoff:3.500A) Processing helix chain 'N' and resid 652 through 669 removed outlier: 3.905A pdb=" N LEU N 662 " --> pdb=" O HIS N 658 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN N 668 " --> pdb=" O ALA N 664 " (cutoff:3.500A) Processing helix chain 'N' and resid 681 through 686 Processing helix chain 'N' and resid 687 through 689 No H-bonds generated for 'chain 'N' and resid 687 through 689' Processing helix chain 'Q' and resid 34 through 45 removed outlier: 5.576A pdb=" N ASN Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY Q 43 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 66 Proline residue: Q 63 - end of helix Processing helix chain 'Q' and resid 79 through 81 No H-bonds generated for 'chain 'Q' and resid 79 through 81' Processing helix chain 'Q' and resid 82 through 87 removed outlier: 4.120A pdb=" N ARG Q 86 " --> pdb=" O HIS Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 103 removed outlier: 4.243A pdb=" N PHE Q 101 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 183 removed outlier: 3.721A pdb=" N LYS Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA Q 181 " --> pdb=" O GLN Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 197 removed outlier: 3.601A pdb=" N GLY Q 197 " --> pdb=" O VAL Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 304 removed outlier: 3.705A pdb=" N ASN Q 300 " --> pdb=" O TRP Q 296 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG Q 301 " --> pdb=" O HIS Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 353 removed outlier: 4.000A pdb=" N MET Q 353 " --> pdb=" O GLN Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 354 through 369 Processing helix chain 'Q' and resid 370 through 372 No H-bonds generated for 'chain 'Q' and resid 370 through 372' Processing helix chain 'Q' and resid 373 through 378 Processing helix chain 'Q' and resid 391 through 415 removed outlier: 4.108A pdb=" N LEU Q 395 " --> pdb=" O ILE Q 391 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR Q 398 " --> pdb=" O PRO Q 394 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS Q 399 " --> pdb=" O LEU Q 395 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN Q 406 " --> pdb=" O ASN Q 402 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR Q 407 " --> pdb=" O GLN Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 512 through 532 Proline residue: Q 525 - end of helix removed outlier: 3.783A pdb=" N LEU Q 528 " --> pdb=" O ILE Q 524 " (cutoff:3.500A) Processing helix chain 'Q' and resid 617 through 622 Processing helix chain 'Z' and resid 28 through 37 removed outlier: 3.866A pdb=" N PHE Z 35 " --> pdb=" O LEU Z 31 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL Z 36 " --> pdb=" O GLU Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 51 Processing helix chain 'Z' and resid 52 through 55 Processing helix chain 'Z' and resid 56 through 64 Processing helix chain 'Z' and resid 85 through 93 removed outlier: 3.680A pdb=" N GLN Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 102 removed outlier: 4.000A pdb=" N VAL Z 102 " --> pdb=" O GLN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 110 removed outlier: 3.695A pdb=" N ARG Z 110 " --> pdb=" O ALA Z 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 10 through 38 removed outlier: 3.684A pdb=" N ILE H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR H 38 " --> pdb=" O ASN H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 67 removed outlier: 3.582A pdb=" N ASN H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 75 Processing helix chain 'H' and resid 82 through 87 removed outlier: 3.934A pdb=" N ARG H 86 " --> pdb=" O ASN H 82 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 82 through 87' Processing helix chain 'H' and resid 90 through 96 removed outlier: 4.377A pdb=" N GLN H 94 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 107 Processing helix chain 'H' and resid 165 through 181 Processing helix chain 'H' and resid 184 through 189 removed outlier: 3.833A pdb=" N TYR H 187 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR H 188 " --> pdb=" O LYS H 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 57 removed outlier: 3.771A pdb=" N ILE K 31 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP K 38 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASN K 39 " --> pdb=" O GLY K 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP K 40 " --> pdb=" O GLU K 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA K 51 " --> pdb=" O HIS K 47 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR K 57 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 123 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 148 through 153 Processing helix chain 'R' and resid 19 through 27 Processing helix chain 'R' and resid 101 through 106 Processing helix chain 'R' and resid 145 through 154 Processing helix chain 'R' and resid 219 through 237 Processing helix chain 'V' and resid 16 through 29 removed outlier: 3.824A pdb=" N ALA V 20 " --> pdb=" O ASN V 16 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR V 24 " --> pdb=" O ALA V 20 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP V 28 " --> pdb=" O THR V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 32 No H-bonds generated for 'chain 'V' and resid 30 through 32' Processing helix chain 'V' and resid 33 through 38 removed outlier: 3.567A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 62 removed outlier: 4.657A pdb=" N MET V 52 " --> pdb=" O GLY V 48 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA V 53 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU V 54 " --> pdb=" O SER V 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS V 59 " --> pdb=" O SER V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 removed outlier: 4.849A pdb=" N SER V 70 " --> pdb=" O GLU V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 119 removed outlier: 4.329A pdb=" N GLN V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU V 97 " --> pdb=" O ALA V 93 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL V 106 " --> pdb=" O ASP V 102 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TRP V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP V 108 " --> pdb=" O GLU V 104 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP V 115 " --> pdb=" O ASN V 111 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG V 116 " --> pdb=" O GLU V 112 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU V 117 " --> pdb=" O MET V 113 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU V 119 " --> pdb=" O ASP V 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 128 removed outlier: 4.119A pdb=" N LYS a 128 " --> pdb=" O LEU a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 197 Processing helix chain 'a' and resid 200 through 205 Processing helix chain 'a' and resid 206 through 208 No H-bonds generated for 'chain 'a' and resid 206 through 208' Processing helix chain 'a' and resid 221 through 236 removed outlier: 3.876A pdb=" N ARG a 230 " --> pdb=" O ALA a 226 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU a 231 " --> pdb=" O ASN a 227 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA a 232 " --> pdb=" O PHE a 228 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL a 233 " --> pdb=" O GLU a 229 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 266 removed outlier: 4.637A pdb=" N ARG a 258 " --> pdb=" O GLU a 254 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU a 259 " --> pdb=" O SER a 255 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU a 264 " --> pdb=" O HIS a 260 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN a 265 " --> pdb=" O ALA a 261 " (cutoff:3.500A) Processing helix chain 'a' and resid 276 through 281 Processing helix chain 'a' and resid 282 through 284 No H-bonds generated for 'chain 'a' and resid 282 through 284' Processing helix chain 'a' and resid 713 through 717 removed outlier: 3.720A pdb=" N ARG a 716 " --> pdb=" O ASP a 713 " (cutoff:3.500A) Processing helix chain 'a' and resid 719 through 725 removed outlier: 3.511A pdb=" N ASP a 723 " --> pdb=" O GLU a 719 " (cutoff:3.500A) Processing helix chain 'b' and resid 474 through 493 removed outlier: 4.302A pdb=" N UNK b 478 " --> pdb=" O UNK b 474 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N UNK b 479 " --> pdb=" O UNK b 475 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N UNK b 483 " --> pdb=" O UNK b 479 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK b 493 " --> pdb=" O UNK b 489 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 24 Processing helix chain 'c' and resid 28 through 41 removed outlier: 4.413A pdb=" N UNK c 32 " --> pdb=" O UNK c 28 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNK c 34 " --> pdb=" O UNK c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 67 Processing helix chain 'c' and resid 79 through 100 removed outlier: 4.035A pdb=" N UNK c 87 " --> pdb=" O UNK c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 115 Processing helix chain 'c' and resid 116 through 119 Processing helix chain 'c' and resid 130 through 140 removed outlier: 3.763A pdb=" N UNK c 134 " --> pdb=" O UNK c 130 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK c 140 " --> pdb=" O UNK c 136 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 156 Processing helix chain 'c' and resid 173 through 186 removed outlier: 3.740A pdb=" N UNK c 177 " --> pdb=" O UNK c 173 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N UNK c 178 " --> pdb=" O UNK c 174 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N UNK c 182 " --> pdb=" O UNK c 178 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N UNK c 183 " --> pdb=" O UNK c 179 " (cutoff:3.500A) Processing helix chain 'c' and resid 192 through 204 Processing sheet with id=AA1, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.986A pdb=" N GLY F 124 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR F 109 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL F 122 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 274 through 277 removed outlier: 4.122A pdb=" N GLU N 283 " --> pdb=" O PHE N 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 369 through 370 removed outlier: 3.944A pdb=" N LEU N 369 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE N 380 " --> pdb=" O LYS N 393 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 492 through 493 removed outlier: 3.987A pdb=" N ASP N 512 " --> pdb=" O ASN N 507 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 584 through 585 removed outlier: 3.716A pdb=" N SER N 584 " --> pdb=" O TRP N 598 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP N 598 " --> pdb=" O SER N 584 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 706 through 707 removed outlier: 3.953A pdb=" N TRP N 706 " --> pdb=" O THR N 755 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR N 755 " --> pdb=" O TRP N 706 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 199 through 202 removed outlier: 4.694A pdb=" N GLN Q 199 " --> pdb=" O LYS Q 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 250 through 252 removed outlier: 3.532A pdb=" N SER Q 250 " --> pdb=" O ALA Q 333 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE Q 318 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 427 through 428 Processing sheet with id=AB1, first strand: chain 'Q' and resid 461 through 462 removed outlier: 3.567A pdb=" N THR Q 462 " --> pdb=" O ARG Q 470 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG Q 470 " --> pdb=" O THR Q 462 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'Q' and resid 596 through 599 Processing sheet with id=AB3, first strand: chain 'R' and resid 8 through 9 removed outlier: 3.753A pdb=" N GLY R 9 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP R 208 " --> pdb=" O GLY R 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 61 through 63 Processing sheet with id=AB5, first strand: chain 'a' and resid 161 through 162 removed outlier: 3.682A pdb=" N VAL a 179 " --> pdb=" O LEU a 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 287 through 289 Processing sheet with id=AB7, first strand: chain 'a' and resid 381 through 386 removed outlier: 6.674A pdb=" N ARG a 706 " --> pdb=" O GLU a 382 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 582 through 585 removed outlier: 3.755A pdb=" N SER a 585 " --> pdb=" O MET a 690 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL a 693 " --> pdb=" O LYS a 661 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6975 1.34 - 1.45: 2375 1.45 - 1.57: 11926 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 21381 Sorted by residual: bond pdb=" CA ILE N 785 " pdb=" CB ILE N 785 " ideal model delta sigma weight residual 1.553 1.533 0.020 7.40e-03 1.83e+04 7.21e+00 bond pdb=" CG LEU N 252 " pdb=" CD1 LEU N 252 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 bond pdb=" C LEU H 100 " pdb=" N GLU H 101 " ideal model delta sigma weight residual 1.329 1.297 0.032 1.86e-02 2.89e+03 2.88e+00 bond pdb=" C GLY U 36 " pdb=" N PRO U 37 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.25e-02 6.40e+03 2.56e+00 bond pdb=" N PHE N 299 " pdb=" CA PHE N 299 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.48e+00 ... (remaining 21376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 28046 2.10 - 4.21: 806 4.21 - 6.31: 104 6.31 - 8.42: 59 8.42 - 10.52: 7 Bond angle restraints: 29022 Sorted by residual: angle pdb=" N PRO N 678 " pdb=" CA PRO N 678 " pdb=" CB PRO N 678 " ideal model delta sigma weight residual 103.25 113.49 -10.24 1.05e+00 9.07e-01 9.52e+01 angle pdb=" N PRO N 230 " pdb=" CA PRO N 230 " pdb=" CB PRO N 230 " ideal model delta sigma weight residual 103.08 110.89 -7.81 9.70e-01 1.06e+00 6.48e+01 angle pdb=" N PRO N 231 " pdb=" CA PRO N 231 " pdb=" CB PRO N 231 " ideal model delta sigma weight residual 103.25 111.34 -8.09 1.05e+00 9.07e-01 5.94e+01 angle pdb=" N PRO N 789 " pdb=" CA PRO N 789 " pdb=" CB PRO N 789 " ideal model delta sigma weight residual 103.25 111.28 -8.03 1.05e+00 9.07e-01 5.85e+01 angle pdb=" N PRO N 779 " pdb=" CA PRO N 779 " pdb=" CB PRO N 779 " ideal model delta sigma weight residual 103.25 111.12 -7.87 1.05e+00 9.07e-01 5.61e+01 ... (remaining 29017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 11684 17.72 - 35.45: 1076 35.45 - 53.17: 172 53.17 - 70.89: 24 70.89 - 88.62: 20 Dihedral angle restraints: 12976 sinusoidal: 4490 harmonic: 8486 Sorted by residual: dihedral pdb=" CA LEU N 497 " pdb=" C LEU N 497 " pdb=" N ASP N 498 " pdb=" CA ASP N 498 " ideal model delta harmonic sigma weight residual 180.00 132.35 47.65 0 5.00e+00 4.00e-02 9.08e+01 dihedral pdb=" CA SER N 435 " pdb=" C SER N 435 " pdb=" N GLN N 436 " pdb=" CA GLN N 436 " ideal model delta harmonic sigma weight residual -180.00 -142.16 -37.84 0 5.00e+00 4.00e-02 5.73e+01 dihedral pdb=" CA LEU K 154 " pdb=" C LEU K 154 " pdb=" N PRO K 155 " pdb=" CA PRO K 155 " ideal model delta harmonic sigma weight residual 180.00 144.41 35.59 0 5.00e+00 4.00e-02 5.07e+01 ... (remaining 12973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2908 0.065 - 0.130: 418 0.130 - 0.196: 32 0.196 - 0.261: 33 0.261 - 0.326: 3 Chirality restraints: 3394 Sorted by residual: chirality pdb=" CB THR Q 464 " pdb=" CA THR Q 464 " pdb=" OG1 THR Q 464 " pdb=" CG2 THR Q 464 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA PRO K 24 " pdb=" N PRO K 24 " pdb=" C PRO K 24 " pdb=" CB PRO K 24 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO N 108 " pdb=" N PRO N 108 " pdb=" C PRO N 108 " pdb=" CB PRO N 108 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 3391 not shown) Planarity restraints: 3801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY U 36 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO U 37 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO U 37 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO U 37 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 47 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LEU D 47 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU D 47 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS D 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 206 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO Q 207 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO Q 207 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO Q 207 " -0.033 5.00e-02 4.00e+02 ... (remaining 3798 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 661 2.68 - 3.24: 23126 3.24 - 3.79: 30900 3.79 - 4.35: 37870 4.35 - 4.90: 57495 Nonbonded interactions: 150052 Sorted by model distance: nonbonded pdb=" OG1 THR N 268 " pdb=" OG1 THR N 275 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR V 26 " pdb=" O LYS V 63 " model vdw 2.135 3.040 nonbonded pdb=" OG SER Q 417 " pdb=" O ARG Q 420 " model vdw 2.159 3.040 nonbonded pdb=" OE2 GLU Q 206 " pdb=" OG1 THR Q 209 " model vdw 2.182 3.040 nonbonded pdb=" O TRP a 324 " pdb=" ND2 ASN a 328 " model vdw 2.185 3.120 ... (remaining 150047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.070 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.004 0.066 21381 Z= 0.194 Angle : 0.897 10.522 29022 Z= 0.541 Chirality : 0.051 0.326 3394 Planarity : 0.005 0.078 3801 Dihedral : 14.323 88.618 7414 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.92 % Allowed : 15.88 % Favored : 83.20 % Rotamer: Outliers : 0.27 % Allowed : 7.32 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.33 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.13), residues: 2607 helix: -2.19 (0.14), residues: 1024 sheet: -3.85 (0.24), residues: 295 loop : -4.61 (0.14), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 113 TYR 0.013 0.001 TYR F 44 PHE 0.016 0.002 PHE U 19 TRP 0.020 0.002 TRP a 378 HIS 0.008 0.001 HIS U 30 Details of bonding type rmsd covalent geometry : bond 0.00370 (21381) covalent geometry : angle 0.89656 (29022) hydrogen bonds : bond 0.13794 ( 839) hydrogen bonds : angle 6.00428 ( 2436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 292 time to evaluate : 0.608 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 Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: F 39 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7117 (ttt180) REVERT: F 80 MET cc_start: 0.7240 (mmm) cc_final: 0.6873 (ttt) REVERT: N 254 LEU cc_start: 0.9288 (tp) cc_final: 0.9042 (tp) REVERT: N 286 LEU cc_start: 0.8236 (tt) cc_final: 0.7655 (tt) REVERT: N 638 MET cc_start: 0.8298 (mmm) cc_final: 0.7951 (mmm) REVERT: N 665 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8714 (tm-30) REVERT: Q 97 TYR cc_start: 0.7609 (m-80) cc_final: 0.7348 (m-80) REVERT: Z 104 ASP cc_start: 0.8843 (t0) cc_final: 0.8210 (t0) REVERT: H 59 ARG cc_start: 0.8946 (mtp85) cc_final: 0.8681 (tpp80) REVERT: H 64 LEU cc_start: 0.9125 (mt) cc_final: 0.8693 (mt) REVERT: V 69 LEU cc_start: 0.8929 (tp) cc_final: 0.8661 (tt) REVERT: V 122 MET cc_start: 0.5619 (ttp) cc_final: 0.4506 (ttm) REVERT: a 210 LEU cc_start: 0.7491 (pt) cc_final: 0.7245 (pp) REVERT: a 217 LEU cc_start: 0.9150 (mp) cc_final: 0.8761 (tp) REVERT: a 659 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8656 (pttt) outliers start: 11 outliers final: 8 residues processed: 303 average time/residue: 0.1767 time to fit residues: 77.3147 Evaluate side-chains 190 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.0050 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 7 GLN D 61 GLN F 21 ASN F 60 ASN G 148 GLN N 253 GLN N 296 GLN ** N 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 375 ASN N 428 GLN N 653 ASN ** N 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 696 GLN Q 309 GLN Q 358 ASN ** Q 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN a 260 HIS a 391 GLN a 622 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.062596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.053146 restraints weight = 198165.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.054085 restraints weight = 121769.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.054744 restraints weight = 85882.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.055181 restraints weight = 66374.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055497 restraints weight = 55038.877| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21381 Z= 0.142 Angle : 0.741 9.433 29022 Z= 0.381 Chirality : 0.045 0.284 3394 Planarity : 0.005 0.075 3801 Dihedral : 6.398 46.208 3049 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.08 % Favored : 85.42 % Rotamer: Outliers : 0.42 % Allowed : 6.37 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.33 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.15), residues: 2607 helix: -0.73 (0.16), residues: 1030 sheet: -3.39 (0.26), residues: 275 loop : -4.13 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 370 TYR 0.018 0.002 TYR N 709 PHE 0.024 0.002 PHE N 299 TRP 0.024 0.002 TRP N 298 HIS 0.007 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00306 (21381) covalent geometry : angle 0.74093 (29022) hydrogen bonds : bond 0.04469 ( 839) hydrogen bonds : angle 5.06518 ( 2436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: U 18 MET cc_start: 0.8302 (tmm) cc_final: 0.7865 (tmm) REVERT: U 122 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8444 (mt-10) REVERT: D 111 ASP cc_start: 0.8401 (t0) cc_final: 0.8096 (t0) REVERT: F 39 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7353 (ttt180) REVERT: F 64 MET cc_start: 0.7707 (tpt) cc_final: 0.7440 (ttp) REVERT: F 80 MET cc_start: 0.7308 (mmm) cc_final: 0.7060 (ttt) REVERT: N 254 LEU cc_start: 0.9284 (tp) cc_final: 0.9058 (tp) REVERT: N 638 MET cc_start: 0.8378 (mmm) cc_final: 0.8112 (mmm) REVERT: N 665 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8791 (tm-30) REVERT: Q 83 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8410 (mp0) REVERT: Q 97 TYR cc_start: 0.7750 (m-80) cc_final: 0.7494 (m-80) REVERT: H 59 ARG cc_start: 0.8903 (mtp85) cc_final: 0.8592 (tpp80) REVERT: K 53 LYS cc_start: 0.9423 (tptm) cc_final: 0.8951 (mttp) REVERT: V 66 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7774 (mp0) REVERT: V 69 LEU cc_start: 0.9267 (tp) cc_final: 0.8903 (tt) REVERT: V 122 MET cc_start: 0.5543 (ttp) cc_final: 0.4927 (ttm) REVERT: a 648 PHE cc_start: 0.8381 (m-10) cc_final: 0.7899 (m-10) REVERT: a 659 LYS cc_start: 0.8951 (ptpp) cc_final: 0.8614 (pttt) outliers start: 14 outliers final: 10 residues processed: 269 average time/residue: 0.1717 time to fit residues: 67.7431 Evaluate side-chains 191 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 270 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 181 optimal weight: 0.0770 chunk 143 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** N 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 388 HIS N 653 ASN ** N 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 ASN Z 121 HIS H 55 GLN K 46 GLN V 111 ASN a 651 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.060692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051196 restraints weight = 199132.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052127 restraints weight = 122852.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052762 restraints weight = 86726.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.053194 restraints weight = 67242.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053506 restraints weight = 55856.186| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21381 Z= 0.197 Angle : 0.773 10.556 29022 Z= 0.398 Chirality : 0.046 0.269 3394 Planarity : 0.005 0.078 3801 Dihedral : 6.468 44.440 3049 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.38 % Allowed : 16.49 % Favored : 83.12 % Rotamer: Outliers : 0.42 % Allowed : 7.11 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.33 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.16), residues: 2607 helix: -0.36 (0.17), residues: 1025 sheet: -3.16 (0.28), residues: 259 loop : -3.92 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 370 TYR 0.019 0.002 TYR N 673 PHE 0.019 0.002 PHE K 105 TRP 0.019 0.002 TRP N 395 HIS 0.006 0.001 HIS Q 297 Details of bonding type rmsd covalent geometry : bond 0.00429 (21381) covalent geometry : angle 0.77307 (29022) hydrogen bonds : bond 0.04735 ( 839) hydrogen bonds : angle 5.12193 ( 2436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 9 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6793 (pt0) REVERT: U 18 MET cc_start: 0.8195 (tmm) cc_final: 0.7729 (tmm) REVERT: D 53 HIS cc_start: 0.8965 (m90) cc_final: 0.8571 (m90) REVERT: F 39 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7405 (ttt180) REVERT: F 64 MET cc_start: 0.7874 (tpt) cc_final: 0.7545 (ttp) REVERT: F 80 MET cc_start: 0.7450 (mmm) cc_final: 0.7163 (ttt) REVERT: N 557 LYS cc_start: 0.9086 (mppt) cc_final: 0.8814 (mmtt) REVERT: N 638 MET cc_start: 0.8463 (mmm) cc_final: 0.8200 (mmm) REVERT: N 665 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8792 (tm-30) REVERT: Q 97 TYR cc_start: 0.7819 (m-80) cc_final: 0.7529 (m-80) REVERT: Q 160 MET cc_start: 0.9078 (ttm) cc_final: 0.8869 (ttm) REVERT: Q 286 MET cc_start: 0.8009 (ttm) cc_final: 0.7809 (ttm) REVERT: H 59 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8644 (tpp80) REVERT: K 53 LYS cc_start: 0.9371 (tptm) cc_final: 0.8909 (mttp) REVERT: V 122 MET cc_start: 0.5523 (ttp) cc_final: 0.4957 (ttm) REVERT: a 648 PHE cc_start: 0.8494 (m-10) cc_final: 0.7978 (m-10) outliers start: 15 outliers final: 12 residues processed: 242 average time/residue: 0.1609 time to fit residues: 57.7075 Evaluate side-chains 184 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 271 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 28 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 29 HIS U 64 GLN U 114 GLN D 119 ASN ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN N 354 HIS ** N 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.061508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.052161 restraints weight = 199061.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.053074 restraints weight = 124822.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.053696 restraints weight = 88895.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054124 restraints weight = 69326.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054434 restraints weight = 57760.613| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21381 Z= 0.149 Angle : 0.725 11.370 29022 Z= 0.370 Chirality : 0.046 0.300 3394 Planarity : 0.005 0.075 3801 Dihedral : 6.247 45.471 3049 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.73 % Favored : 84.96 % Rotamer: Outliers : 0.27 % Allowed : 5.10 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.33 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.16), residues: 2607 helix: -0.10 (0.17), residues: 1043 sheet: -2.92 (0.28), residues: 262 loop : -3.94 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 59 TYR 0.016 0.001 TYR N 673 PHE 0.034 0.002 PHE G 112 TRP 0.015 0.001 TRP Z 120 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00328 (21381) covalent geometry : angle 0.72469 (29022) hydrogen bonds : bond 0.04223 ( 839) hydrogen bonds : angle 4.94647 ( 2436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.840 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 Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 130 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 9 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6826 (pt0) REVERT: D 13 GLU cc_start: 0.9080 (pp20) cc_final: 0.8775 (pm20) REVERT: D 53 HIS cc_start: 0.9075 (m90) cc_final: 0.8655 (m90) REVERT: F 39 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7460 (ttt180) REVERT: F 64 MET cc_start: 0.7695 (tpt) cc_final: 0.7407 (ttp) REVERT: F 135 MET cc_start: 0.8518 (tmm) cc_final: 0.8304 (tpp) REVERT: G 119 LYS cc_start: 0.9091 (pttt) cc_final: 0.8794 (pttm) REVERT: N 286 LEU cc_start: 0.8024 (mp) cc_final: 0.7431 (mp) REVERT: N 557 LYS cc_start: 0.9012 (mppt) cc_final: 0.8748 (mmtt) REVERT: N 665 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8750 (tm-30) REVERT: Q 97 TYR cc_start: 0.7908 (m-80) cc_final: 0.7655 (m-80) REVERT: Q 286 MET cc_start: 0.8058 (ttm) cc_final: 0.7830 (ttm) REVERT: Z 114 MET cc_start: 0.5445 (ttm) cc_final: 0.5120 (ttt) REVERT: H 59 ARG cc_start: 0.9034 (mtp85) cc_final: 0.8597 (tpp80) REVERT: V 66 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7828 (mp0) REVERT: V 122 MET cc_start: 0.5480 (ttp) cc_final: 0.4949 (ttm) REVERT: a 648 PHE cc_start: 0.8511 (m-10) cc_final: 0.7936 (m-10) outliers start: 13 outliers final: 11 residues processed: 255 average time/residue: 0.1657 time to fit residues: 62.0125 Evaluate side-chains 190 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 155 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 7 GLN U 114 GLN ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 148 GLN ** N 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.062066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.052766 restraints weight = 197576.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.053686 restraints weight = 123851.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054318 restraints weight = 88213.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.054750 restraints weight = 68744.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.055068 restraints weight = 57121.551| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21381 Z= 0.131 Angle : 0.709 10.556 29022 Z= 0.359 Chirality : 0.045 0.266 3394 Planarity : 0.005 0.107 3801 Dihedral : 5.962 44.826 3049 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.46 % Favored : 85.23 % Rotamer: Outliers : 0.21 % Allowed : 4.72 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.33 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.16), residues: 2607 helix: 0.05 (0.17), residues: 1051 sheet: -2.74 (0.28), residues: 273 loop : -3.89 (0.15), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 710 TYR 0.026 0.001 TYR F 44 PHE 0.029 0.002 PHE U 19 TRP 0.016 0.001 TRP Z 120 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00291 (21381) covalent geometry : angle 0.70896 (29022) hydrogen bonds : bond 0.03927 ( 839) hydrogen bonds : angle 4.82110 ( 2436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.656 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 Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 130 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash REVERT: U 9 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6770 (pt0) REVERT: U 122 GLU cc_start: 0.8832 (pt0) cc_final: 0.8609 (pp20) REVERT: D 13 GLU cc_start: 0.9024 (pp20) cc_final: 0.8721 (pm20) REVERT: D 53 HIS cc_start: 0.9074 (m90) cc_final: 0.8662 (m90) REVERT: D 117 SER cc_start: 0.9122 (p) cc_final: 0.8671 (m) REVERT: F 39 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7719 (ttt180) REVERT: F 80 MET cc_start: 0.7443 (mmm) cc_final: 0.7214 (ttt) REVERT: F 135 MET cc_start: 0.8451 (tmm) cc_final: 0.8222 (tpp) REVERT: G 112 PHE cc_start: 0.7989 (m-80) cc_final: 0.7722 (m-80) REVERT: N 254 LEU cc_start: 0.9186 (tp) cc_final: 0.8876 (tp) REVERT: N 286 LEU cc_start: 0.7579 (mp) cc_final: 0.7274 (mp) REVERT: N 557 LYS cc_start: 0.9017 (mppt) cc_final: 0.8737 (mmtt) REVERT: N 665 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8779 (tm-30) REVERT: N 669 LEU cc_start: 0.7801 (mm) cc_final: 0.6802 (mm) REVERT: Q 97 TYR cc_start: 0.7754 (m-80) cc_final: 0.7521 (m-80) REVERT: Q 232 ARG cc_start: 0.8506 (pmt170) cc_final: 0.8251 (ppt170) REVERT: Q 286 MET cc_start: 0.8039 (ttm) cc_final: 0.7712 (ttm) REVERT: H 59 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8583 (tpp80) REVERT: V 122 MET cc_start: 0.5489 (ttp) cc_final: 0.4914 (ttm) REVERT: a 207 ASP cc_start: 0.7927 (t70) cc_final: 0.7664 (t0) outliers start: 12 outliers final: 11 residues processed: 249 average time/residue: 0.1596 time to fit residues: 59.6864 Evaluate side-chains 196 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 62 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 114 GLN D 61 GLN ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN N 354 HIS ** N 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 367 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.062459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053151 restraints weight = 196539.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054074 restraints weight = 123619.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.054701 restraints weight = 88031.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.055143 restraints weight = 68634.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055451 restraints weight = 57121.884| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21381 Z= 0.128 Angle : 0.704 11.706 29022 Z= 0.355 Chirality : 0.044 0.245 3394 Planarity : 0.005 0.071 3801 Dihedral : 5.817 45.073 3049 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.77 % Favored : 85.88 % Rotamer: Outliers : 0.21 % Allowed : 3.34 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.67 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.17), residues: 2607 helix: 0.24 (0.17), residues: 1025 sheet: -2.59 (0.29), residues: 249 loop : -3.72 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 136 TYR 0.018 0.001 TYR F 44 PHE 0.051 0.002 PHE N 299 TRP 0.020 0.001 TRP F 196 HIS 0.013 0.001 HIS N 354 Details of bonding type rmsd covalent geometry : bond 0.00283 (21381) covalent geometry : angle 0.70414 (29022) hydrogen bonds : bond 0.03702 ( 839) hydrogen bonds : angle 4.72225 ( 2436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.734 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 Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 130 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 9 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6804 (pt0) REVERT: U 122 GLU cc_start: 0.8849 (pt0) cc_final: 0.8588 (pp20) REVERT: D 13 GLU cc_start: 0.9017 (pp20) cc_final: 0.8773 (pm20) REVERT: D 117 SER cc_start: 0.9124 (p) cc_final: 0.8716 (m) REVERT: F 39 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7621 (ttt180) REVERT: F 146 MET cc_start: 0.8428 (ppp) cc_final: 0.7879 (ppp) REVERT: G 119 LYS cc_start: 0.8941 (pttt) cc_final: 0.8607 (pttm) REVERT: N 254 LEU cc_start: 0.9116 (tp) cc_final: 0.8714 (tp) REVERT: N 286 LEU cc_start: 0.7587 (mp) cc_final: 0.7367 (mp) REVERT: N 557 LYS cc_start: 0.9002 (mppt) cc_final: 0.8715 (mmtt) REVERT: N 665 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8677 (tm-30) REVERT: Q 83 GLU cc_start: 0.8613 (mp0) cc_final: 0.8353 (mp0) REVERT: H 59 ARG cc_start: 0.9023 (mtp85) cc_final: 0.8717 (tpp-160) REVERT: K 53 LYS cc_start: 0.9390 (tptm) cc_final: 0.8807 (mtmt) REVERT: V 66 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7826 (mt-10) REVERT: V 122 MET cc_start: 0.5464 (ttp) cc_final: 0.4909 (ttm) REVERT: a 207 ASP cc_start: 0.7851 (t70) cc_final: 0.7541 (t0) REVERT: a 648 PHE cc_start: 0.8374 (m-10) cc_final: 0.8080 (m-10) outliers start: 12 outliers final: 11 residues processed: 251 average time/residue: 0.1609 time to fit residues: 60.0282 Evaluate side-chains 194 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 267 optimal weight: 10.0000 chunk 167 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 161 optimal weight: 0.0770 chunk 168 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 252 optimal weight: 0.4980 chunk 124 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 84 optimal weight: 0.0570 overall best weight: 0.2666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 114 GLN D 57 HIS F 21 ASN ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** N 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.063540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.054222 restraints weight = 197140.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.055191 restraints weight = 122034.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.055855 restraints weight = 86126.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056310 restraints weight = 66504.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.056635 restraints weight = 54995.439| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21381 Z= 0.124 Angle : 0.697 12.747 29022 Z= 0.347 Chirality : 0.044 0.230 3394 Planarity : 0.005 0.069 3801 Dihedral : 5.520 44.354 3049 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.62 % Favored : 86.08 % Rotamer: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.17), residues: 2607 helix: 0.33 (0.17), residues: 1036 sheet: -2.29 (0.30), residues: 249 loop : -3.72 (0.15), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 707 TYR 0.029 0.001 TYR Q 97 PHE 0.030 0.001 PHE U 19 TRP 0.021 0.001 TRP Z 120 HIS 0.005 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00270 (21381) covalent geometry : angle 0.69699 (29022) hydrogen bonds : bond 0.03394 ( 839) hydrogen bonds : angle 4.53441 ( 2436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 248 time to evaluate : 0.704 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 Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 130 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 189 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 122 GLU cc_start: 0.8797 (pt0) cc_final: 0.8569 (pp20) REVERT: D 13 GLU cc_start: 0.9038 (pp20) cc_final: 0.8817 (pm20) REVERT: D 117 SER cc_start: 0.9047 (p) cc_final: 0.8754 (m) REVERT: F 39 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7763 (ttt180) REVERT: F 135 MET cc_start: 0.8154 (tpp) cc_final: 0.7759 (tpp) REVERT: F 146 MET cc_start: 0.8297 (ppp) cc_final: 0.7819 (ppp) REVERT: G 112 PHE cc_start: 0.8025 (m-80) cc_final: 0.7773 (m-80) REVERT: G 119 LYS cc_start: 0.8933 (pttt) cc_final: 0.8575 (pttm) REVERT: N 254 LEU cc_start: 0.9145 (tp) cc_final: 0.8825 (tp) REVERT: N 286 LEU cc_start: 0.7584 (mp) cc_final: 0.7252 (mp) REVERT: N 557 LYS cc_start: 0.8980 (mppt) cc_final: 0.8709 (mmtt) REVERT: N 665 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8672 (tm-30) REVERT: H 59 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8421 (tpp80) REVERT: K 53 LYS cc_start: 0.9356 (tptm) cc_final: 0.8799 (mtmt) REVERT: V 14 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7337 (mtm-85) REVERT: V 122 MET cc_start: 0.5469 (ttp) cc_final: 0.4899 (ttm) REVERT: a 648 PHE cc_start: 0.8340 (m-10) cc_final: 0.7942 (m-10) outliers start: 13 outliers final: 12 residues processed: 261 average time/residue: 0.1600 time to fit residues: 62.3129 Evaluate side-chains 199 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 123 optimal weight: 0.0670 chunk 269 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 152 optimal weight: 0.2980 chunk 172 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 114 GLN D 57 HIS ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 GLN Q 367 HIS Z 92 GLN a 196 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.063263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054043 restraints weight = 197899.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.054985 restraints weight = 124380.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.055598 restraints weight = 88255.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056054 restraints weight = 68904.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056380 restraints weight = 57246.466| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21381 Z= 0.124 Angle : 0.711 13.169 29022 Z= 0.354 Chirality : 0.044 0.245 3394 Planarity : 0.005 0.068 3801 Dihedral : 5.451 43.946 3049 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.46 % Favored : 86.23 % Rotamer: Outliers : 0.21 % Allowed : 2.02 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.17), residues: 2607 helix: 0.37 (0.17), residues: 1041 sheet: -2.18 (0.30), residues: 268 loop : -3.71 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 157 TYR 0.019 0.001 TYR Q 97 PHE 0.063 0.002 PHE N 299 TRP 0.019 0.001 TRP F 196 HIS 0.009 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00274 (21381) covalent geometry : angle 0.71084 (29022) hydrogen bonds : bond 0.03435 ( 839) hydrogen bonds : angle 4.53550 ( 2436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 0.790 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 Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 130 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 189 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 9 GLN cc_start: 0.8815 (pt0) cc_final: 0.8054 (mm-40) REVERT: U 18 MET cc_start: 0.8142 (tmm) cc_final: 0.7941 (tmm) REVERT: U 122 GLU cc_start: 0.8841 (pt0) cc_final: 0.8607 (pp20) REVERT: D 13 GLU cc_start: 0.9050 (pp20) cc_final: 0.8798 (pm20) REVERT: D 117 SER cc_start: 0.9026 (p) cc_final: 0.8739 (m) REVERT: F 80 MET cc_start: 0.7315 (mmm) cc_final: 0.7113 (ttt) REVERT: F 135 MET cc_start: 0.8231 (tpp) cc_final: 0.7871 (tpp) REVERT: F 146 MET cc_start: 0.8485 (ppp) cc_final: 0.7925 (ppp) REVERT: G 112 PHE cc_start: 0.8124 (m-80) cc_final: 0.7832 (m-80) REVERT: G 119 LYS cc_start: 0.8836 (pttt) cc_final: 0.8595 (pttp) REVERT: N 254 LEU cc_start: 0.9114 (tp) cc_final: 0.8808 (tp) REVERT: N 286 LEU cc_start: 0.7534 (mp) cc_final: 0.6882 (mp) REVERT: N 557 LYS cc_start: 0.9006 (mppt) cc_final: 0.8722 (mmtt) REVERT: N 665 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8665 (tm-30) REVERT: Q 286 MET cc_start: 0.8530 (mtp) cc_final: 0.7742 (ttm) REVERT: H 59 ARG cc_start: 0.8813 (mtp85) cc_final: 0.8555 (tpp-160) REVERT: K 53 LYS cc_start: 0.9359 (tptm) cc_final: 0.8770 (mtmt) REVERT: V 14 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7451 (mtm-85) REVERT: V 122 MET cc_start: 0.5389 (ttp) cc_final: 0.4829 (ttm) REVERT: a 648 PHE cc_start: 0.8369 (m-10) cc_final: 0.7978 (m-10) outliers start: 13 outliers final: 12 residues processed: 259 average time/residue: 0.1586 time to fit residues: 61.4545 Evaluate side-chains 205 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 169 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 173 optimal weight: 0.4980 chunk 42 optimal weight: 0.2980 chunk 284 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 252 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 114 GLN ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 GLN ** Q 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.063524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054213 restraints weight = 196624.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.055178 restraints weight = 122505.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.055835 restraints weight = 86549.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.056269 restraints weight = 66960.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056602 restraints weight = 55706.933| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21381 Z= 0.122 Angle : 0.709 12.576 29022 Z= 0.350 Chirality : 0.044 0.249 3394 Planarity : 0.004 0.064 3801 Dihedral : 5.344 45.983 3049 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.85 % Favored : 85.85 % Rotamer: Outliers : 0.16 % Allowed : 1.17 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.17), residues: 2607 helix: 0.47 (0.17), residues: 1030 sheet: -2.07 (0.30), residues: 275 loop : -3.64 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 157 TYR 0.015 0.001 TYR Q 97 PHE 0.019 0.001 PHE U 19 TRP 0.025 0.001 TRP V 107 HIS 0.004 0.001 HIS a 651 Details of bonding type rmsd covalent geometry : bond 0.00269 (21381) covalent geometry : angle 0.70857 (29022) hydrogen bonds : bond 0.03369 ( 839) hydrogen bonds : angle 4.47519 ( 2436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 130 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 189 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: U 9 GLN cc_start: 0.8816 (pt0) cc_final: 0.7999 (mm-40) REVERT: U 24 PHE cc_start: 0.8533 (t80) cc_final: 0.8293 (t80) REVERT: U 122 GLU cc_start: 0.8827 (pt0) cc_final: 0.8588 (pp20) REVERT: D 13 GLU cc_start: 0.9059 (pp20) cc_final: 0.8818 (pm20) REVERT: D 51 GLU cc_start: 0.8994 (mp0) cc_final: 0.8778 (pm20) REVERT: D 117 SER cc_start: 0.8938 (p) cc_final: 0.8682 (m) REVERT: F 64 MET cc_start: 0.8337 (ptm) cc_final: 0.7859 (ptm) REVERT: F 135 MET cc_start: 0.8273 (tpp) cc_final: 0.7903 (tpp) REVERT: F 146 MET cc_start: 0.8454 (ppp) cc_final: 0.7939 (ppp) REVERT: G 112 PHE cc_start: 0.8126 (m-80) cc_final: 0.7790 (m-80) REVERT: G 119 LYS cc_start: 0.8823 (pttt) cc_final: 0.8586 (pttp) REVERT: N 254 LEU cc_start: 0.9097 (tp) cc_final: 0.8699 (tp) REVERT: N 267 TYR cc_start: 0.6752 (m-10) cc_final: 0.6274 (m-10) REVERT: N 286 LEU cc_start: 0.7638 (mp) cc_final: 0.7296 (mp) REVERT: N 557 LYS cc_start: 0.9010 (mppt) cc_final: 0.8729 (mmtt) REVERT: N 665 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8648 (tm-30) REVERT: Q 286 MET cc_start: 0.8523 (mtp) cc_final: 0.7727 (ttm) REVERT: H 59 ARG cc_start: 0.8782 (mtp85) cc_final: 0.8454 (tpp80) REVERT: V 122 MET cc_start: 0.5405 (ttp) cc_final: 0.4736 (ttm) REVERT: a 648 PHE cc_start: 0.8406 (m-10) cc_final: 0.8111 (m-10) outliers start: 12 outliers final: 12 residues processed: 254 average time/residue: 0.1583 time to fit residues: 60.0555 Evaluate side-chains 202 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 85 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 206 optimal weight: 0.4980 chunk 230 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 176 optimal weight: 0.0170 chunk 272 optimal weight: 9.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 114 GLN D 53 HIS ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN N 505 GLN ** Q 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.063409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054047 restraints weight = 197632.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.055004 restraints weight = 123418.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.055656 restraints weight = 87426.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056076 restraints weight = 67920.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.056432 restraints weight = 56473.815| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21381 Z= 0.124 Angle : 0.710 11.742 29022 Z= 0.351 Chirality : 0.044 0.236 3394 Planarity : 0.004 0.062 3801 Dihedral : 5.306 46.910 3049 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.46 % Favored : 86.23 % Rotamer: Outliers : 0.16 % Allowed : 0.90 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.17), residues: 2607 helix: 0.56 (0.17), residues: 1036 sheet: -1.96 (0.31), residues: 268 loop : -3.68 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 157 TYR 0.017 0.001 TYR N 545 PHE 0.031 0.001 PHE U 19 TRP 0.029 0.001 TRP V 107 HIS 0.005 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00272 (21381) covalent geometry : angle 0.71011 (29022) hydrogen bonds : bond 0.03333 ( 839) hydrogen bonds : angle 4.44992 ( 2436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.682 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 Corrupt residue: chain: R residue: PRO 2 >>> skipping Corrupt residue: chain: R residue: PRO 52 >>> skipping Corrupt residue: chain: R residue: PRO 95 >>> skipping Corrupt residue: chain: R residue: PRO 104 >>> skipping Corrupt residue: chain: R residue: PRO 122 >>> skipping Corrupt residue: chain: R residue: PRO 130 >>> skipping Corrupt residue: chain: R residue: PRO 131 >>> skipping Corrupt residue: chain: R residue: PRO 189 >>> skipping Corrupt residue: chain: R residue: PRO 203 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: U 9 GLN cc_start: 0.8803 (pt0) cc_final: 0.7998 (mm-40) REVERT: U 24 PHE cc_start: 0.8535 (t80) cc_final: 0.8291 (t80) REVERT: U 122 GLU cc_start: 0.8816 (pt0) cc_final: 0.8545 (pp20) REVERT: D 13 GLU cc_start: 0.9069 (pp20) cc_final: 0.8844 (pm20) REVERT: D 117 SER cc_start: 0.8943 (p) cc_final: 0.8735 (m) REVERT: F 135 MET cc_start: 0.8282 (tpp) cc_final: 0.7912 (tpp) REVERT: G 119 LYS cc_start: 0.8851 (pttt) cc_final: 0.8607 (pttp) REVERT: N 254 LEU cc_start: 0.9144 (tp) cc_final: 0.8752 (tp) REVERT: N 267 TYR cc_start: 0.6802 (m-10) cc_final: 0.6323 (m-10) REVERT: N 557 LYS cc_start: 0.9010 (mppt) cc_final: 0.8724 (mmtt) REVERT: N 665 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8657 (tm-30) REVERT: Q 286 MET cc_start: 0.8532 (mtp) cc_final: 0.7760 (ttm) REVERT: H 59 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8466 (tpp80) REVERT: V 66 GLU cc_start: 0.7894 (mp0) cc_final: 0.7665 (mp0) REVERT: V 122 MET cc_start: 0.5456 (ttp) cc_final: 0.4787 (ttm) REVERT: a 648 PHE cc_start: 0.8366 (m-10) cc_final: 0.8033 (m-10) outliers start: 12 outliers final: 12 residues processed: 250 average time/residue: 0.1557 time to fit residues: 58.5986 Evaluate side-chains 195 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 42 optimal weight: 0.0570 chunk 59 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 152 optimal weight: 0.0770 chunk 93 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 114 GLN D 53 HIS D 61 GLN ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 367 HIS ** 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 = 0.3586 r_free = 0.3586 target = 0.063857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.054551 restraints weight = 197868.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055533 restraints weight = 122885.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.056165 restraints weight = 86525.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.056629 restraints weight = 67266.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.056953 restraints weight = 55643.876| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21381 Z= 0.119 Angle : 0.701 11.517 29022 Z= 0.346 Chirality : 0.044 0.233 3394 Planarity : 0.004 0.060 3801 Dihedral : 5.187 46.107 3049 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.12 % Favored : 86.57 % Rotamer: Outliers : 0.16 % Allowed : 0.80 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.17), residues: 2607 helix: 0.57 (0.17), residues: 1035 sheet: -1.88 (0.31), residues: 267 loop : -3.68 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 157 TYR 0.025 0.001 TYR N 545 PHE 0.027 0.001 PHE U 19 TRP 0.030 0.001 TRP V 107 HIS 0.004 0.001 HIS a 651 Details of bonding type rmsd covalent geometry : bond 0.00263 (21381) covalent geometry : angle 0.70124 (29022) hydrogen bonds : bond 0.03221 ( 839) hydrogen bonds : angle 4.43566 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4208.13 seconds wall clock time: 72 minutes 53.07 seconds (4373.07 seconds total)