Starting phenix.real_space_refine on Sun Sep 13 08:59:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.map" model { file = "/net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h25_0128/09_2026/6h25_0128.cif" } resolution = 3.8 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= 0.008 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 126 5.16 5 C 13910 2.51 5 N 3938 2.21 5 O 4158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22138 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2221 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1771 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 231} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1923 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'TYR:plan': 2, 'ARG:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1570 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 202} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2144 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1752 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1527 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2066 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "I" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 373 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 6488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6488 Classifications: {'peptide': 868} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 43, 'TRANS': 824} Chain breaks: 3 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 28, 'GLN:plan1': 5, 'ASP:plan': 15, 'ASN:plan1': 4, 'ARG:plan': 11, 'HIS:plan': 5, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 295 Chain: "K" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 183 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNAv2': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 4.96, per 1000 atoms: 0.22 Number of scatterers: 22138 At special positions: 0 Unit cell: (137.7, 143.1, 152.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 6 15.00 O 4158 8.00 N 3938 7.00 C 13910 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: 1.82 Conformation dependent library (CDL) restraints added in 949.7 milliseconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 40 sheets defined 31.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.636A pdb=" N LEU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.627A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 243 through 277 removed outlier: 3.887A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.882A pdb=" N ALA B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 110 removed outlier: 4.500A pdb=" N SER B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.641A pdb=" N LEU B 115 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 150 Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.531A pdb=" N GLY B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 244 removed outlier: 3.853A pdb=" N ASP B 229 " --> pdb=" O HIS B 225 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.517A pdb=" N GLN C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.511A pdb=" N ASP C 123 " --> pdb=" O GLN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.694A pdb=" N ALA C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 244 through 273 removed outlier: 3.511A pdb=" N LEU C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 128 through 145 removed outlier: 3.767A pdb=" N CYS D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 202 through 232 removed outlier: 3.533A pdb=" N ARG D 225 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.768A pdb=" N LEU E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 147 through 162 removed outlier: 4.270A pdb=" N ALA E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 221 Processing helix chain 'E' and resid 248 through 280 removed outlier: 3.860A pdb=" N ILE E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.320A pdb=" N TYR F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 131 removed outlier: 3.937A pdb=" N GLU F 121 " --> pdb=" O CYS F 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 173 removed outlier: 3.808A pdb=" N ALA F 160 " --> pdb=" O SER F 156 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 233 through 266 Proline residue: F 253 - end of helix removed outlier: 3.653A pdb=" N ARG F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 146 No H-bonds generated for 'chain 'G' and resid 144 through 146' Processing helix chain 'G' and resid 203 through 211 removed outlier: 3.559A pdb=" N ILE G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 225 removed outlier: 3.682A pdb=" N GLU G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 256 Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 175 through 179 removed outlier: 4.174A pdb=" N VAL H 179 " --> pdb=" O PRO H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 247 removed outlier: 3.620A pdb=" N ASN H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 264 Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.715A pdb=" N ILE H 271 " --> pdb=" O ILE H 268 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU H 272 " --> pdb=" O LYS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 291 Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 76 through 81 Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 102 through 115 removed outlier: 3.553A pdb=" N ASN J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 163 Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 194 through 200 Processing helix chain 'J' and resid 203 through 207 removed outlier: 3.989A pdb=" N GLU J 206 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 298 through 302 removed outlier: 3.512A pdb=" N TRP J 302 " --> pdb=" O LYS J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 437 removed outlier: 3.768A pdb=" N HIS J 437 " --> pdb=" O LEU J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 451 removed outlier: 3.529A pdb=" N SER J 450 " --> pdb=" O GLN J 446 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE J 451 " --> pdb=" O ALA J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 464 removed outlier: 3.686A pdb=" N ASP J 463 " --> pdb=" O THR J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 517 through 527 Processing helix chain 'J' and resid 541 through 547 Processing helix chain 'J' and resid 589 through 599 Processing helix chain 'J' and resid 604 through 628 removed outlier: 3.589A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE J 625 " --> pdb=" O LYS J 621 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU J 626 " --> pdb=" O LYS J 622 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY J 628 " --> pdb=" O ARG J 624 " (cutoff:3.500A) Processing helix chain 'J' and resid 657 through 683 removed outlier: 4.225A pdb=" N SER J 661 " --> pdb=" O ARG J 657 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER J 683 " --> pdb=" O HIS J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 709 removed outlier: 3.702A pdb=" N ILE J 701 " --> pdb=" O SER J 697 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU J 702 " --> pdb=" O ASN J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 717 through 727 Processing helix chain 'J' and resid 733 through 747 removed outlier: 3.954A pdb=" N ASN J 737 " --> pdb=" O PHE J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 781 through 795 removed outlier: 3.543A pdb=" N VAL J 785 " --> pdb=" O ARG J 781 " (cutoff:3.500A) Processing helix chain 'J' and resid 801 through 805 Processing helix chain 'J' and resid 806 through 842 removed outlier: 3.599A pdb=" N LEU J 810 " --> pdb=" O ASP J 806 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 822 " --> pdb=" O ASN J 818 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET J 823 " --> pdb=" O PHE J 819 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN J 825 " --> pdb=" O HIS J 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR J 826 " --> pdb=" O LYS J 822 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 885 Processing helix chain 'K' and resid 82 through 96 removed outlier: 3.758A pdb=" N LYS K 86 " --> pdb=" O PRO K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.391A pdb=" N ILE A 75 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 134 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 77 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU A 136 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN A 79 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 138 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLU A 81 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.805A pdb=" N TRP A 130 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS A 122 " --> pdb=" O TRP A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.704A pdb=" N TYR A 204 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 220 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER A 236 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 222 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 234 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 224 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR A 233 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 203 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN A 235 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET B 201 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A 237 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N LEU B 199 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 195 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA B 188 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 199 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 201 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN B 184 " --> pdb=" O MET B 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 6.264A pdb=" N LYS B 47 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 71 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE B 123 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 73 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL B 125 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 75 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL B 127 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER B 77 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLN B 129 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.394A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP C 133 " --> pdb=" O CYS C 125 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS C 125 " --> pdb=" O TRP C 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 84 removed outlier: 7.130A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 174 through 178 removed outlier: 4.600A pdb=" N GLU C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.394A pdb=" N THR C 223 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU C 235 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 225 " --> pdb=" O CYS C 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.208A pdb=" N SER D 53 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 117 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER D 115 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR D 75 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL D 118 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU D 77 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU D 120 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 79 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL D 122 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG D 81 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N SER D 124 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.555A pdb=" N ASP D 186 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU D 192 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 67 removed outlier: 6.676A pdb=" N TRP E 133 " --> pdb=" O CYS E 125 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS E 125 " --> pdb=" O TRP E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 78 through 85 removed outlier: 7.542A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLU E 143 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP E 57 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL E 35 " --> pdb=" O ARG H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 210 through 212 removed outlier: 4.229A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 229 " --> pdb=" O CYS E 238 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N CYS E 238 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 239 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU F 225 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY E 243 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ALA F 223 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA F 214 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU F 225 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 212 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY F 227 " --> pdb=" O GLY F 210 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY F 210 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.628A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS F 61 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 145 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN F 143 " --> pdb=" O PRO F 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 144 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL F 146 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 27 through 28 removed outlier: 3.948A pdb=" N GLY G 84 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG G 85 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP G 103 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AC1, first strand: chain 'G' and resid 191 through 192 removed outlier: 7.000A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER G 140 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS G 124 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS G 130 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 165 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 199 through 201 removed outlier: 4.096A pdb=" N LEU G 227 " --> pdb=" O PHE K 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE K 77 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'H' and resid 164 through 165 removed outlier: 7.110A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 156 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU H 109 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG H 95 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL H 91 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS H 97 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AC7, first strand: chain 'I' and resid 7 through 8 removed outlier: 8.016A pdb=" N VAL I 55 " --> pdb=" O GLY I 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 13 through 15 removed outlier: 7.028A pdb=" N ILE I 33 " --> pdb=" O LEU I 14 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 2 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 66 through 68 removed outlier: 5.721A pdb=" N PHE J 173 " --> pdb=" O PHE J 192 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 87 through 91 removed outlier: 7.036A pdb=" N VAL J 88 " --> pdb=" O TYR J 121 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE J 123 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL J 90 " --> pdb=" O PHE J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 274 through 278 removed outlier: 7.540A pdb=" N ILE J 291 " --> pdb=" O ILE J 348 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 348 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA J 293 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 356 through 361 removed outlier: 3.805A pdb=" N LEU J 372 " --> pdb=" O SER J 361 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG J 384 " --> pdb=" O GLY J 414 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE J 416 " --> pdb=" O ARG J 384 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN J 413 " --> pdb=" O ASP J 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 417 " --> pdb=" O ILE J 399 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE J 399 " --> pdb=" O VAL J 417 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASN J 419 " --> pdb=" O ARG J 397 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ARG J 397 " --> pdb=" O ASN J 419 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG J 396 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU J 360 " --> pdb=" O ARG J 396 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 468 through 469 removed outlier: 6.464A pdb=" N GLU J 468 " --> pdb=" O VAL J 581 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN J 583 " --> pdb=" O GLU J 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS J 574 " --> pdb=" O GLU J 565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 476 through 478 removed outlier: 6.517A pdb=" N SER J 477 " --> pdb=" O LEU J 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 530 through 531 Processing sheet with id=AD8, first strand: chain 'J' and resid 638 through 640 Processing sheet with id=AD9, first strand: chain 'J' and resid 687 through 690 Processing sheet with id=AE1, first strand: chain 'J' and resid 847 through 848 removed outlier: 3.620A pdb=" N GLU J 848 " --> pdb=" O VAL J 909 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 909 " --> pdb=" O GLU J 848 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 851 through 855 removed outlier: 7.011A pdb=" N VAL J 861 " --> pdb=" O LEU J 853 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL J 855 " --> pdb=" O ALA J 859 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA J 859 " --> pdb=" O VAL J 855 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 886 through 887 removed outlier: 3.643A pdb=" N LEU J 894 " --> pdb=" O PHE J 901 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 912 through 914 removed outlier: 3.554A pdb=" N LYS J 922 " --> pdb=" O ASP J 914 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2871 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: 4.84 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3750 1.31 - 1.44: 5445 1.44 - 1.57: 13124 1.57 - 1.69: 12 1.69 - 1.82: 172 Bond restraints: 22503 Sorted by residual: bond pdb=" C ILE B 25 " pdb=" O ILE B 25 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.07e-02 8.73e+03 2.36e+01 bond pdb=" N PRO J 883 " pdb=" CD PRO J 883 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO J 770 " pdb=" CD PRO J 770 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO J 802 " pdb=" CD PRO J 802 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO J 881 " pdb=" CD PRO J 881 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 ... (remaining 22498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 29958 3.15 - 6.29: 538 6.29 - 9.44: 57 9.44 - 12.59: 13 12.59 - 15.74: 7 Bond angle restraints: 30573 Sorted by residual: angle pdb=" N GLU E 181 " pdb=" CA GLU E 181 " pdb=" C GLU E 181 " ideal model delta sigma weight residual 111.07 126.81 -15.74 1.07e+00 8.73e-01 2.16e+02 angle pdb=" CA PRO J 802 " pdb=" N PRO J 802 " pdb=" CD PRO J 802 " ideal model delta sigma weight residual 112.00 98.29 13.71 1.40e+00 5.10e-01 9.59e+01 angle pdb=" CA PRO J 883 " pdb=" N PRO J 883 " pdb=" CD PRO J 883 " ideal model delta sigma weight residual 112.00 98.31 13.69 1.40e+00 5.10e-01 9.56e+01 angle pdb=" CA PRO J 881 " pdb=" N PRO J 881 " pdb=" CD PRO J 881 " ideal model delta sigma weight residual 112.00 98.46 13.54 1.40e+00 5.10e-01 9.36e+01 angle pdb=" CA PRO J 770 " pdb=" N PRO J 770 " pdb=" CD PRO J 770 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.14e+01 ... (remaining 30568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 12841 15.75 - 31.51: 615 31.51 - 47.26: 196 47.26 - 63.01: 15 63.01 - 78.77: 13 Dihedral angle restraints: 13680 sinusoidal: 5128 harmonic: 8552 Sorted by residual: dihedral pdb=" C4' U R 39 " pdb=" C3' U R 39 " pdb=" C2' U R 39 " pdb=" C1' U R 39 " ideal model delta sinusoidal sigma weight residual 36.34 -40.43 76.77 1 3.10e+00 1.04e-01 7.70e+02 dihedral pdb=" O4' U R 39 " pdb=" C4' U R 39 " pdb=" C3' U R 39 " pdb=" C2' U R 39 " ideal model delta sinusoidal sigma weight residual -35.15 39.12 -74.27 1 4.00e+00 6.25e-02 4.37e+02 dihedral pdb=" O4' U R 39 " pdb=" C2' U R 39 " pdb=" C1' U R 39 " pdb=" C3' U R 39 " ideal model delta sinusoidal sigma weight residual 25.59 -28.12 53.72 3 3.80e+00 6.93e-02 1.44e+02 ... (remaining 13677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3477 0.124 - 0.249: 137 0.249 - 0.373: 10 0.373 - 0.497: 2 0.497 - 0.622: 1 Chirality restraints: 3627 Sorted by residual: chirality pdb=" CA GLU E 181 " pdb=" N GLU E 181 " pdb=" C GLU E 181 " pdb=" CB GLU E 181 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" CA ASN J 603 " pdb=" N ASN J 603 " pdb=" C ASN J 603 " pdb=" CB ASN J 603 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA LYS J 118 " pdb=" N LYS J 118 " pdb=" C LYS J 118 " pdb=" CB LYS J 118 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 3624 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 23 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG C 23 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 23 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 23 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 23 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 880 " -0.128 5.00e-02 4.00e+02 1.80e-01 5.17e+01 pdb=" N PRO J 881 " 0.310 5.00e-02 4.00e+02 pdb=" CA PRO J 881 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO J 881 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 882 " 0.104 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO J 883 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO J 883 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO J 883 " 0.074 5.00e-02 4.00e+02 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 5 1.86 - 2.62: 246 2.62 - 3.38: 27378 3.38 - 4.14: 48735 4.14 - 4.90: 85953 Nonbonded interactions: 162317 Sorted by model distance: nonbonded pdb=" OG SER J 599 " pdb=" OD1 ASN J 601 " model vdw 1.101 3.040 nonbonded pdb=" CE2 PHE J 840 " pdb=" CG2 ILE J 911 " model vdw 1.407 3.760 nonbonded pdb=" O ARG K 78 " pdb=" N PHE K 80 " model vdw 1.583 3.120 nonbonded pdb=" NE2 GLN J 837 " pdb=" O GLN J 921 " model vdw 1.641 3.120 nonbonded pdb=" CD LYS A 267 " pdb=" OE2 GLU A 286 " model vdw 1.808 3.440 ... (remaining 162312 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.530 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.006 0.081 22503 Z= 0.327 Angle : 1.098 15.735 30573 Z= 0.648 Chirality : 0.060 0.622 3627 Planarity : 0.011 0.448 3956 Dihedral : 10.938 78.768 8146 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.67 % Favored : 93.92 % Rotamer: Outliers : 1.51 % Allowed : 4.45 % Favored : 94.04 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.13), residues: 2929 helix: -1.64 (0.14), residues: 842 sheet: -0.65 (0.20), residues: 639 loop : -2.55 (0.13), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 17 TYR 0.024 0.003 TYR C 136 PHE 0.029 0.003 PHE J 451 TRP 0.054 0.004 TRP J 405 HIS 0.011 0.002 HIS J 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.33 (22503) covalent geometry : angle 1.09807 / 0.65 (30573) hydrogen bonds : bond 0.17185 / 11.42 ( 995) hydrogen bonds : angle 6.75730 / 4.75 ( 2871) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 898 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8164 (tp30) cc_final: 0.7803 (tp30) REVERT: A 20 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8418 (tm-30) REVERT: A 107 GLU cc_start: 0.7995 (tt0) cc_final: 0.7773 (tt0) REVERT: A 114 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7898 (mmtp) REVERT: A 171 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7707 (mm-30) REVERT: A 181 ASP cc_start: 0.8020 (m-30) cc_final: 0.7471 (p0) REVERT: A 186 SER cc_start: 0.8351 (m) cc_final: 0.7469 (p) REVERT: A 188 HIS cc_start: 0.8357 (m-70) cc_final: 0.7946 (m-70) REVERT: A 225 MET cc_start: 0.8019 (mtp) cc_final: 0.7201 (mtp) REVERT: A 228 HIS cc_start: 0.8773 (m90) cc_final: 0.8511 (m-70) REVERT: A 229 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7115 (ttm-80) REVERT: A 263 GLU cc_start: 0.8338 (tp30) cc_final: 0.8036 (tm-30) REVERT: B 15 ASP cc_start: 0.8152 (m-30) cc_final: 0.7797 (m-30) REVERT: B 21 GLU cc_start: 0.8285 (pt0) cc_final: 0.8013 (pt0) REVERT: B 36 ASP cc_start: 0.8173 (t0) cc_final: 0.7801 (t0) REVERT: B 69 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7604 (ptm160) REVERT: B 75 GLN cc_start: 0.8078 (tt0) cc_final: 0.7553 (tt0) REVERT: B 82 SER cc_start: 0.7424 (t) cc_final: 0.7152 (p) REVERT: B 118 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8002 (mtp85) REVERT: B 131 ASP cc_start: 0.7774 (t0) cc_final: 0.7410 (t70) REVERT: B 155 ASP cc_start: 0.7989 (t0) cc_final: 0.7549 (t0) REVERT: B 201 MET cc_start: 0.5273 (tmm) cc_final: 0.4985 (tmm) REVERT: B 223 ASP cc_start: 0.7328 (m-30) cc_final: 0.7004 (m-30) REVERT: B 242 LEU cc_start: 0.8545 (mt) cc_final: 0.8306 (mt) REVERT: C 38 ASN cc_start: 0.7517 (m-40) cc_final: 0.7118 (m110) REVERT: C 60 CYS cc_start: 0.8452 (t) cc_final: 0.8108 (t) REVERT: C 74 PRO cc_start: 0.8003 (Cg_endo) cc_final: 0.7619 (Cg_exo) REVERT: C 75 ASP cc_start: 0.8116 (p0) cc_final: 0.6504 (t0) REVERT: C 92 ARG cc_start: 0.8870 (ptp-170) cc_final: 0.8537 (mtp-110) REVERT: C 101 GLU cc_start: 0.8197 (tp30) cc_final: 0.7798 (tp30) REVERT: C 127 SER cc_start: 0.8161 (t) cc_final: 0.7856 (p) REVERT: C 131 LEU cc_start: 0.8570 (mt) cc_final: 0.8324 (mt) REVERT: C 134 VAL cc_start: 0.7917 (t) cc_final: 0.7553 (p) REVERT: C 147 ASN cc_start: 0.8356 (t160) cc_final: 0.7592 (t0) REVERT: C 209 ASP cc_start: 0.8026 (t0) cc_final: 0.7745 (t0) REVERT: C 227 ASP cc_start: 0.7217 (t0) cc_final: 0.6178 (t70) REVERT: C 234 CYS cc_start: 0.8142 (p) cc_final: 0.7780 (t) REVERT: C 247 LYS cc_start: 0.7394 (tppt) cc_final: 0.7020 (mmtt) REVERT: C 272 SER cc_start: 0.8446 (t) cc_final: 0.8137 (m) REVERT: C 273 MET cc_start: 0.7909 (mmt) cc_final: 0.7693 (tmm) REVERT: C 274 LYS cc_start: 0.7865 (tttt) cc_final: 0.7587 (mmtt) REVERT: D 29 ARG cc_start: 0.6180 (pmt100) cc_final: 0.5934 (ptt90) REVERT: D 53 SER cc_start: 0.7808 (t) cc_final: 0.7209 (p) REVERT: D 110 LEU cc_start: 0.8502 (tp) cc_final: 0.8155 (mp) REVERT: D 149 ARG cc_start: 0.7701 (ptp-170) cc_final: 0.7500 (ptp-110) REVERT: D 168 ASP cc_start: 0.8520 (m-30) cc_final: 0.7985 (t0) REVERT: D 190 ARG cc_start: 0.8753 (mpt-90) cc_final: 0.8470 (mtt-85) REVERT: D 203 ASP cc_start: 0.7686 (p0) cc_final: 0.7360 (p0) REVERT: E 6 LEU cc_start: 0.7845 (pp) cc_final: 0.7601 (pp) REVERT: E 11 LYS cc_start: 0.7766 (mttt) cc_final: 0.7525 (mttt) REVERT: E 75 ASN cc_start: 0.8374 (p0) cc_final: 0.7525 (p0) REVERT: E 144 CYS cc_start: 0.8226 (t) cc_final: 0.7310 (m) REVERT: E 164 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7980 (mtt-85) REVERT: E 195 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7815 (pm20) REVERT: E 211 VAL cc_start: 0.8358 (t) cc_final: 0.8153 (p) REVERT: E 287 VAL cc_start: 0.8098 (t) cc_final: 0.7850 (p) REVERT: F 40 TYR cc_start: 0.7356 (t80) cc_final: 0.6820 (t80) REVERT: F 64 CYS cc_start: 0.8277 (m) cc_final: 0.7599 (m) REVERT: F 101 ARG cc_start: 0.7616 (mtt-85) cc_final: 0.7392 (mtp85) REVERT: F 108 ARG cc_start: 0.8576 (mtt90) cc_final: 0.8194 (mtt-85) REVERT: F 143 GLN cc_start: 0.7608 (pt0) cc_final: 0.7052 (pt0) REVERT: F 147 SER cc_start: 0.8000 (t) cc_final: 0.7752 (m) REVERT: F 152 GLU cc_start: 0.7610 (tt0) cc_final: 0.7171 (tt0) REVERT: F 178 ASP cc_start: 0.8459 (t0) cc_final: 0.8165 (t70) REVERT: F 194 THR cc_start: 0.8753 (m) cc_final: 0.8383 (p) REVERT: F 204 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F 220 ASN cc_start: 0.8244 (t0) cc_final: 0.8029 (t0) REVERT: F 234 THR cc_start: 0.8221 (m) cc_final: 0.7759 (p) REVERT: G 32 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7726 (mt-10) REVERT: G 77 ARG cc_start: 0.5223 (mtt180) cc_final: 0.4942 (mtt180) REVERT: G 156 ASN cc_start: 0.7988 (p0) cc_final: 0.7722 (t0) REVERT: G 157 VAL cc_start: 0.7817 (t) cc_final: 0.7509 (m) REVERT: G 178 MET cc_start: 0.5968 (ptm) cc_final: 0.4907 (ptt) REVERT: G 220 GLU cc_start: 0.5276 (tt0) cc_final: 0.5072 (tt0) REVERT: G 236 ARG cc_start: 0.6500 (ttm170) cc_final: 0.6204 (mtt180) REVERT: G 253 ILE cc_start: 0.7232 (mt) cc_final: 0.6934 (tp) REVERT: H 6 ARG cc_start: 0.7572 (ptp-170) cc_final: 0.7145 (ptt-90) REVERT: H 49 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7679 (pt0) REVERT: H 61 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6723 (mt-10) REVERT: H 82 ASP cc_start: 0.7536 (m-30) cc_final: 0.7312 (m-30) REVERT: H 87 ARG cc_start: 0.7135 (ttm-80) cc_final: 0.6174 (ttm-80) REVERT: H 95 ARG cc_start: 0.6552 (pmt100) cc_final: 0.6256 (ptt-90) REVERT: H 99 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6157 (tm-30) REVERT: H 112 SER cc_start: 0.8267 (m) cc_final: 0.7778 (p) REVERT: H 140 LEU cc_start: 0.7124 (mt) cc_final: 0.6810 (mt) REVERT: H 165 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7925 (tttt) REVERT: H 180 LYS cc_start: 0.7665 (mtpm) cc_final: 0.6975 (mtmt) REVERT: H 246 THR cc_start: 0.7977 (m) cc_final: 0.7648 (p) REVERT: H 247 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7250 (mm110) REVERT: H 249 MET cc_start: 0.8390 (ttt) cc_final: 0.8088 (ttm) REVERT: H 251 LEU cc_start: 0.8035 (tt) cc_final: 0.7774 (tt) REVERT: H 260 TYR cc_start: 0.7236 (t80) cc_final: 0.6963 (t80) REVERT: I 16 ASN cc_start: 0.6364 (m-40) cc_final: 0.5452 (p0) REVERT: J 22 GLU cc_start: 0.8028 (pt0) cc_final: 0.7523 (pt0) REVERT: J 69 ASP cc_start: 0.7381 (t0) cc_final: 0.6865 (t70) REVERT: J 82 ASP cc_start: 0.6554 (t70) cc_final: 0.6271 (t70) REVERT: J 102 SER cc_start: 0.6440 (t) cc_final: 0.6105 (p) REVERT: J 122 THR cc_start: 0.8274 (m) cc_final: 0.8033 (t) REVERT: J 169 LEU cc_start: 0.8391 (mt) cc_final: 0.8186 (mp) REVERT: J 170 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7017 (tt0) REVERT: J 175 THR cc_start: 0.8717 (t) cc_final: 0.8508 (p) REVERT: J 259 LEU cc_start: 0.8307 (mt) cc_final: 0.8088 (mm) REVERT: J 285 ARG cc_start: 0.4733 (ptp-170) cc_final: 0.4527 (ptp90) REVERT: J 357 CYS cc_start: 0.8010 (m) cc_final: 0.7771 (m) REVERT: J 367 GLU cc_start: 0.8440 (mp0) cc_final: 0.8151 (mp0) REVERT: J 379 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7199 (mtm-85) REVERT: J 474 CYS cc_start: 0.4610 (p) cc_final: 0.4284 (m) REVERT: J 522 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7786 (tt0) REVERT: J 569 ASN cc_start: 0.8874 (m-40) cc_final: 0.8642 (t0) REVERT: J 588 LEU cc_start: 0.6211 (mt) cc_final: 0.5868 (mt) REVERT: J 602 MET cc_start: 0.3969 (OUTLIER) cc_final: 0.3426 (mtt) REVERT: J 624 ARG cc_start: 0.8775 (ttp-170) cc_final: 0.8367 (tpm170) REVERT: J 665 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5768 (mm-30) REVERT: J 667 MET cc_start: 0.8317 (mmp) cc_final: 0.7909 (mmm) REVERT: J 671 ASN cc_start: 0.7827 (m-40) cc_final: 0.7580 (m110) REVERT: J 676 LYS cc_start: 0.7368 (mttt) cc_final: 0.7094 (tttp) REVERT: J 712 GLU cc_start: 0.4598 (OUTLIER) cc_final: 0.4088 (pp20) REVERT: J 735 TYR cc_start: 0.7418 (t80) cc_final: 0.6910 (t80) REVERT: J 748 MET cc_start: 0.6172 (mmp) cc_final: 0.5940 (mmm) REVERT: J 841 LYS cc_start: 0.5403 (OUTLIER) cc_final: 0.4922 (tppp) REVERT: J 925 MET cc_start: 0.6986 (mmt) cc_final: 0.6716 (mmt) outliers start: 34 outliers final: 12 residues processed: 925 average time/residue: 0.1765 time to fit residues: 242.1156 Evaluate side-chains 631 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 616 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 601 ASN Chi-restraints excluded: chain J residue 602 MET Chi-restraints excluded: chain J residue 687 LEU Chi-restraints excluded: chain J residue 712 GLU Chi-restraints excluded: chain J residue 750 GLN Chi-restraints excluded: chain J residue 800 THR Chi-restraints excluded: chain J residue 838 LEU Chi-restraints excluded: chain J residue 839 PHE Chi-restraints excluded: chain J residue 841 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 141 HIS A 159 HIS A 189 HIS B 43 GLN B 102 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 192 HIS D 30 HIS D 229 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN E 285 GLN F 143 GLN F 257 GLN H 185 HIS J 43 HIS J 92 GLN J 127 HIS J 146 ASN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 HIS J 288 HIS J 415 HIS J 737 ASN J 750 GLN J 763 HIS J 825 GLN J 828 GLN J 835 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.177224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148444 restraints weight = 31106.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148890 restraints weight = 20668.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.150239 restraints weight = 15481.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.150974 restraints weight = 13077.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151242 restraints weight = 11179.301| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22503 Z= 0.164 Angle : 0.686 9.076 30573 Z= 0.351 Chirality : 0.046 0.443 3627 Planarity : 0.005 0.070 3956 Dihedral : 7.187 162.658 3290 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 4.63 % Allowed : 13.30 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 2929 helix: 0.38 (0.17), residues: 851 sheet: -0.36 (0.19), residues: 675 loop : -2.05 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 249 TYR 0.019 0.002 TYR H 206 PHE 0.023 0.002 PHE D 221 TRP 0.018 0.002 TRP J 155 HIS 0.005 0.001 HIS J 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (22503) covalent geometry : angle 0.68638 / 0.35 (30573) hydrogen bonds : bond 0.04819 / 3.19 ( 995) hydrogen bonds : angle 4.99097 / 3.52 ( 2871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 658 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9156 (tt) REVERT: A 190 MET cc_start: 0.8396 (mtm) cc_final: 0.7911 (mtt) REVERT: A 199 PHE cc_start: 0.8143 (m-80) cc_final: 0.7904 (m-80) REVERT: A 208 ASP cc_start: 0.8118 (t0) cc_final: 0.7769 (t0) REVERT: A 217 MET cc_start: 0.9053 (ptt) cc_final: 0.8803 (ptt) REVERT: A 225 MET cc_start: 0.8471 (mtp) cc_final: 0.8169 (mtp) REVERT: B 101 LEU cc_start: 0.8868 (mt) cc_final: 0.8412 (mt) REVERT: B 155 ASP cc_start: 0.8497 (t0) cc_final: 0.8253 (t0) REVERT: B 156 PHE cc_start: 0.8659 (t80) cc_final: 0.8431 (t80) REVERT: B 198 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 242 LEU cc_start: 0.8934 (mt) cc_final: 0.8689 (mt) REVERT: C 38 ASN cc_start: 0.8093 (m-40) cc_final: 0.7834 (m110) REVERT: C 60 CYS cc_start: 0.8003 (t) cc_final: 0.7737 (t) REVERT: C 75 ASP cc_start: 0.7506 (p0) cc_final: 0.7258 (t0) REVERT: C 83 VAL cc_start: 0.9238 (t) cc_final: 0.8948 (p) REVERT: C 115 ASN cc_start: 0.8499 (m-40) cc_final: 0.8243 (m-40) REVERT: C 162 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7828 (t0) REVERT: C 167 GLU cc_start: 0.7542 (tt0) cc_final: 0.7054 (tt0) REVERT: C 227 ASP cc_start: 0.8192 (t0) cc_final: 0.7968 (t0) REVERT: D 110 LEU cc_start: 0.8947 (tp) cc_final: 0.8641 (mp) REVERT: E 32 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: F 143 GLN cc_start: 0.8212 (pt0) cc_final: 0.7793 (pt0) REVERT: F 176 MET cc_start: 0.8577 (mtp) cc_final: 0.8293 (mtt) REVERT: F 194 THR cc_start: 0.8877 (m) cc_final: 0.8644 (p) REVERT: F 226 LEU cc_start: 0.9287 (tp) cc_final: 0.9062 (tt) REVERT: F 239 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6404 (tp30) REVERT: G 29 LEU cc_start: 0.8569 (mt) cc_final: 0.8292 (mt) REVERT: G 113 LYS cc_start: 0.6508 (tttp) cc_final: 0.6255 (tttp) REVERT: G 157 VAL cc_start: 0.8320 (t) cc_final: 0.8085 (m) REVERT: G 253 ILE cc_start: 0.8448 (mt) cc_final: 0.7958 (tp) REVERT: H 99 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7410 (tp30) REVERT: H 247 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7786 (mm-40) REVERT: I 16 ASN cc_start: 0.8352 (m-40) cc_final: 0.6898 (p0) REVERT: J 110 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8200 (tpp80) REVERT: J 285 ARG cc_start: 0.6947 (ptp-170) cc_final: 0.6143 (ptt180) REVERT: J 508 ASP cc_start: 0.8510 (t0) cc_final: 0.8211 (t0) REVERT: J 521 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7400 (mt0) REVERT: J 665 GLU cc_start: 0.6522 (mm-30) cc_final: 0.6319 (mm-30) REVERT: J 699 TYR cc_start: 0.5663 (m-80) cc_final: 0.5394 (m-80) REVERT: J 738 THR cc_start: 0.8241 (p) cc_final: 0.8019 (p) REVERT: J 776 THR cc_start: 0.8995 (p) cc_final: 0.8717 (t) REVERT: J 841 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6773 (tppp) REVERT: J 922 LYS cc_start: 0.7271 (ttpt) cc_final: 0.7025 (ptpp) outliers start: 104 outliers final: 56 residues processed: 713 average time/residue: 0.1553 time to fit residues: 171.6739 Evaluate side-chains 591 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 530 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 510 SER Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 785 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 841 LYS Chi-restraints excluded: chain J residue 875 PHE Chi-restraints excluded: chain J residue 918 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 145 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 228 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 34 ASN B 102 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN D 30 HIS D 49 GLN D 173 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN H 157 HIS H 185 HIS ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 763 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.146327 restraints weight = 31089.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146427 restraints weight = 20556.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147813 restraints weight = 15574.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148676 restraints weight = 13001.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.148822 restraints weight = 11201.678| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22503 Z= 0.143 Angle : 0.628 8.832 30573 Z= 0.318 Chirality : 0.044 0.245 3627 Planarity : 0.004 0.054 3956 Dihedral : 6.607 177.648 3269 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 4.98 % Allowed : 17.70 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2929 helix: 1.18 (0.17), residues: 851 sheet: -0.33 (0.19), residues: 669 loop : -1.75 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 924 TYR 0.014 0.001 TYR H 206 PHE 0.019 0.002 PHE C 154 TRP 0.030 0.002 TRP J 302 HIS 0.010 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (22503) covalent geometry : angle 0.62786 / 0.32 (30573) hydrogen bonds : bond 0.04127 / 2.74 ( 995) hydrogen bonds : angle 4.59183 / 3.24 ( 2871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 581 time to evaluate : 0.907 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8928 (mttt) cc_final: 0.8492 (pttm) REVERT: A 98 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9123 (tt) REVERT: A 171 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7722 (mt-10) REVERT: A 190 MET cc_start: 0.8559 (mtm) cc_final: 0.8056 (mtt) REVERT: A 217 MET cc_start: 0.9058 (ptt) cc_final: 0.8652 (ptt) REVERT: A 242 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8979 (pp) REVERT: A 281 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7262 (mptt) REVERT: C 60 CYS cc_start: 0.8008 (t) cc_final: 0.7746 (t) REVERT: C 75 ASP cc_start: 0.7675 (p0) cc_final: 0.7320 (t0) REVERT: C 83 VAL cc_start: 0.9246 (t) cc_final: 0.8962 (p) REVERT: C 115 ASN cc_start: 0.8540 (m-40) cc_final: 0.8275 (m-40) REVERT: C 167 GLU cc_start: 0.7300 (tt0) cc_final: 0.6629 (tt0) REVERT: C 189 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 273 MET cc_start: 0.7935 (tmm) cc_final: 0.7729 (tmm) REVERT: D 110 LEU cc_start: 0.9013 (tp) cc_final: 0.8717 (mp) REVERT: D 193 LEU cc_start: 0.9333 (mt) cc_final: 0.8998 (mt) REVERT: E 32 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: F 143 GLN cc_start: 0.8400 (pt0) cc_final: 0.7789 (pt0) REVERT: F 176 MET cc_start: 0.8647 (mtp) cc_final: 0.8357 (mtt) REVERT: F 194 THR cc_start: 0.8775 (m) cc_final: 0.8535 (p) REVERT: G 113 LYS cc_start: 0.6728 (tttp) cc_final: 0.6297 (tttp) REVERT: G 253 ILE cc_start: 0.8431 (mt) cc_final: 0.7943 (tp) REVERT: H 49 GLU cc_start: 0.6831 (pt0) cc_final: 0.6027 (pt0) REVERT: H 99 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7339 (tp30) REVERT: H 131 MET cc_start: 0.7130 (ttp) cc_final: 0.6836 (ttp) REVERT: I 16 ASN cc_start: 0.8398 (m-40) cc_final: 0.6879 (p0) REVERT: J 110 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8558 (tpp80) REVERT: J 259 LEU cc_start: 0.9130 (mm) cc_final: 0.8899 (mp) REVERT: J 521 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7487 (mt0) REVERT: J 545 SER cc_start: 0.9095 (t) cc_final: 0.8884 (p) REVERT: J 748 MET cc_start: 0.6989 (mmp) cc_final: 0.6563 (mmm) REVERT: J 749 MET cc_start: 0.7186 (tpp) cc_final: 0.6972 (tpp) REVERT: J 826 TYR cc_start: 0.8406 (m-80) cc_final: 0.8132 (m-80) REVERT: J 920 HIS cc_start: 0.8231 (m-70) cc_final: 0.7909 (m-70) outliers start: 112 outliers final: 73 residues processed: 651 average time/residue: 0.1527 time to fit residues: 155.3490 Evaluate side-chains 605 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 528 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 435 LEU Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 131 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 166 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN C 162 ASN D 30 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN G 245 GLN H 185 HIS ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 231 HIS J 788 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.174549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145055 restraints weight = 31426.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144820 restraints weight = 21447.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.146656 restraints weight = 15811.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147557 restraints weight = 12610.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.147868 restraints weight = 11375.413| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22503 Z= 0.122 Angle : 0.598 9.297 30573 Z= 0.300 Chirality : 0.043 0.243 3627 Planarity : 0.004 0.056 3956 Dihedral : 6.319 175.581 3265 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 4.80 % Allowed : 19.44 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 2929 helix: 1.59 (0.18), residues: 852 sheet: -0.05 (0.20), residues: 636 loop : -1.55 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 6 TYR 0.013 0.001 TYR H 252 PHE 0.017 0.001 PHE D 221 TRP 0.012 0.001 TRP J 564 HIS 0.005 0.001 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (22503) covalent geometry : angle 0.59843 / 0.30 (30573) hydrogen bonds : bond 0.03744 / 2.48 ( 995) hydrogen bonds : angle 4.38110 / 3.10 ( 2871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 572 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8879 (mttt) cc_final: 0.8408 (pttm) REVERT: A 98 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9095 (tt) REVERT: A 103 ASN cc_start: 0.9084 (t0) cc_final: 0.8681 (t0) REVERT: A 171 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7577 (tt0) REVERT: A 190 MET cc_start: 0.8609 (mtm) cc_final: 0.8157 (mtt) REVERT: A 281 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7216 (mptt) REVERT: C 60 CYS cc_start: 0.8112 (t) cc_final: 0.7777 (t) REVERT: C 75 ASP cc_start: 0.7783 (p0) cc_final: 0.7506 (t0) REVERT: C 83 VAL cc_start: 0.9242 (t) cc_final: 0.8963 (p) REVERT: C 115 ASN cc_start: 0.8634 (m-40) cc_final: 0.8329 (m-40) REVERT: C 236 HIS cc_start: 0.8357 (t70) cc_final: 0.7943 (t70) REVERT: C 273 MET cc_start: 0.7937 (tmm) cc_final: 0.7628 (tmm) REVERT: E 33 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7590 (pmt100) REVERT: E 182 LEU cc_start: 0.8695 (tm) cc_final: 0.8476 (tm) REVERT: F 176 MET cc_start: 0.8606 (mtp) cc_final: 0.8363 (mtt) REVERT: F 194 THR cc_start: 0.8778 (m) cc_final: 0.8505 (p) REVERT: F 250 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7469 (ptp90) REVERT: G 113 LYS cc_start: 0.6638 (tttp) cc_final: 0.6294 (tttp) REVERT: G 168 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8448 (p) REVERT: G 253 ILE cc_start: 0.8380 (mt) cc_final: 0.7895 (tp) REVERT: H 47 MET cc_start: 0.8673 (mmm) cc_final: 0.8062 (mmm) REVERT: H 99 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7254 (tp30) REVERT: H 155 SER cc_start: 0.9056 (t) cc_final: 0.8694 (m) REVERT: I 16 ASN cc_start: 0.8426 (m-40) cc_final: 0.6984 (p0) REVERT: J 110 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8484 (tpp80) REVERT: J 199 LYS cc_start: 0.7720 (mmtm) cc_final: 0.7331 (mmtm) REVERT: J 245 THR cc_start: 0.7615 (p) cc_final: 0.7171 (t) REVERT: J 259 LEU cc_start: 0.9084 (mm) cc_final: 0.8876 (mp) REVERT: J 405 TRP cc_start: 0.8832 (t60) cc_final: 0.8601 (t60) REVERT: J 433 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8505 (tp) REVERT: J 545 SER cc_start: 0.9001 (t) cc_final: 0.8735 (p) REVERT: J 623 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6645 (mtp180) REVERT: J 667 MET cc_start: 0.9271 (mmp) cc_final: 0.8786 (mmt) REVERT: J 748 MET cc_start: 0.7023 (mmp) cc_final: 0.6610 (mmm) REVERT: J 826 TYR cc_start: 0.8360 (m-80) cc_final: 0.8101 (m-80) REVERT: J 841 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6726 (tppp) REVERT: J 920 HIS cc_start: 0.8065 (m-70) cc_final: 0.7817 (m-70) outliers start: 108 outliers final: 74 residues processed: 635 average time/residue: 0.1503 time to fit residues: 150.6332 Evaluate side-chains 598 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 518 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 510 SER Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 841 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 23 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 126 optimal weight: 0.0030 chunk 211 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 188 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN C 162 ASN G 245 GLN H 239 ASN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139543 restraints weight = 31188.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141530 restraints weight = 19247.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.142914 restraints weight = 12991.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143926 restraints weight = 10047.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.143979 restraints weight = 9205.680| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22503 Z= 0.109 Angle : 0.584 11.967 30573 Z= 0.290 Chirality : 0.042 0.284 3627 Planarity : 0.003 0.051 3956 Dihedral : 6.157 178.138 3265 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 4.80 % Allowed : 20.28 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 2929 helix: 1.84 (0.18), residues: 851 sheet: 0.14 (0.20), residues: 626 loop : -1.44 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 92 TYR 0.014 0.001 TYR H 252 PHE 0.029 0.001 PHE E 289 TRP 0.010 0.001 TRP J 155 HIS 0.003 0.001 HIS C 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22503) covalent geometry : angle 0.58414 / 0.29 (30573) hydrogen bonds : bond 0.03500 / 2.32 ( 995) hydrogen bonds : angle 4.23724 / 3.00 ( 2871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 568 time to evaluate : 0.856 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9114 (tt) REVERT: A 103 ASN cc_start: 0.9042 (t0) cc_final: 0.8671 (t0) REVERT: A 171 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7593 (tt0) REVERT: A 190 MET cc_start: 0.8588 (mtm) cc_final: 0.8160 (mtt) REVERT: A 217 MET cc_start: 0.9157 (ptt) cc_final: 0.8551 (ptt) REVERT: A 281 LYS cc_start: 0.7584 (mmmt) cc_final: 0.7167 (mptt) REVERT: B 26 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: B 155 ASP cc_start: 0.8259 (t0) cc_final: 0.7932 (t0) REVERT: C 60 CYS cc_start: 0.8144 (t) cc_final: 0.7785 (t) REVERT: C 75 ASP cc_start: 0.7748 (p0) cc_final: 0.7510 (t0) REVERT: C 83 VAL cc_start: 0.9226 (t) cc_final: 0.8932 (p) REVERT: C 115 ASN cc_start: 0.8605 (m-40) cc_final: 0.8305 (m-40) REVERT: C 122 GLU cc_start: 0.7949 (mp0) cc_final: 0.7637 (mp0) REVERT: C 236 HIS cc_start: 0.8287 (t70) cc_final: 0.7882 (t70) REVERT: C 268 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 273 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7587 (tmm) REVERT: D 193 LEU cc_start: 0.9340 (mt) cc_final: 0.9010 (mt) REVERT: D 230 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7093 (ttm-80) REVERT: E 182 LEU cc_start: 0.8741 (tm) cc_final: 0.8425 (tm) REVERT: F 175 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7293 (mt-10) REVERT: F 176 MET cc_start: 0.8381 (mtp) cc_final: 0.8165 (mtt) REVERT: F 194 THR cc_start: 0.8717 (m) cc_final: 0.8434 (p) REVERT: F 250 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7377 (ptp90) REVERT: G 253 ILE cc_start: 0.8351 (mt) cc_final: 0.7816 (tp) REVERT: H 99 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7266 (tp30) REVERT: H 155 SER cc_start: 0.9038 (t) cc_final: 0.8834 (p) REVERT: I 16 ASN cc_start: 0.8429 (m-40) cc_final: 0.7004 (p0) REVERT: I 57 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7551 (mtp85) REVERT: J 16 VAL cc_start: 0.9521 (OUTLIER) cc_final: 0.9263 (m) REVERT: J 110 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8476 (tpp80) REVERT: J 245 THR cc_start: 0.7817 (p) cc_final: 0.7395 (t) REVERT: J 259 LEU cc_start: 0.9084 (mm) cc_final: 0.8832 (mp) REVERT: J 433 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8550 (tp) REVERT: J 491 HIS cc_start: 0.6076 (OUTLIER) cc_final: 0.5708 (p-80) REVERT: J 623 ARG cc_start: 0.7386 (mtp180) cc_final: 0.6662 (mtp180) REVERT: J 671 ASN cc_start: 0.7755 (m-40) cc_final: 0.7298 (m-40) REVERT: J 749 MET cc_start: 0.6783 (tpp) cc_final: 0.6543 (tpp) REVERT: J 826 TYR cc_start: 0.8349 (m-80) cc_final: 0.8149 (m-80) REVERT: J 919 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7941 (mm-40) outliers start: 108 outliers final: 71 residues processed: 631 average time/residue: 0.1512 time to fit residues: 150.3986 Evaluate side-chains 609 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 529 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 252 TYR Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 491 HIS Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 913 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 53 optimal weight: 0.0970 chunk 277 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 182 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 141 HIS A 235 GLN B 105 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 920 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.176698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147384 restraints weight = 31524.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.147633 restraints weight = 20231.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.149560 restraints weight = 15873.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.150123 restraints weight = 11384.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.150179 restraints weight = 9743.607| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22503 Z= 0.107 Angle : 0.589 13.579 30573 Z= 0.291 Chirality : 0.042 0.278 3627 Planarity : 0.003 0.054 3956 Dihedral : 6.062 178.913 3265 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 4.63 % Allowed : 21.40 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2929 helix: 1.96 (0.18), residues: 856 sheet: 0.23 (0.21), residues: 602 loop : -1.33 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 924 TYR 0.016 0.001 TYR J 753 PHE 0.026 0.001 PHE E 289 TRP 0.009 0.001 TRP J 155 HIS 0.003 0.001 HIS J 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (22503) covalent geometry : angle 0.58938 / 0.29 (30573) hydrogen bonds : bond 0.03424 / 2.26 ( 995) hydrogen bonds : angle 4.20588 / 2.97 ( 2871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 557 time to evaluate : 0.843 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8520 (pttm) REVERT: A 98 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9038 (tt) REVERT: A 103 ASN cc_start: 0.9034 (t0) cc_final: 0.8680 (t0) REVERT: A 108 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8383 (ttm170) REVERT: A 190 MET cc_start: 0.8700 (mtm) cc_final: 0.8314 (mtt) REVERT: A 217 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8577 (ptm) REVERT: A 277 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7453 (pttp) REVERT: A 281 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7005 (mptt) REVERT: B 26 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: B 155 ASP cc_start: 0.8400 (t0) cc_final: 0.8034 (t0) REVERT: C 60 CYS cc_start: 0.8214 (t) cc_final: 0.7803 (t) REVERT: C 75 ASP cc_start: 0.7872 (p0) cc_final: 0.7457 (t0) REVERT: C 83 VAL cc_start: 0.9251 (t) cc_final: 0.8947 (p) REVERT: C 115 ASN cc_start: 0.8634 (m-40) cc_final: 0.8333 (m-40) REVERT: C 122 GLU cc_start: 0.8036 (mp0) cc_final: 0.7668 (mp0) REVERT: C 236 HIS cc_start: 0.8252 (t70) cc_final: 0.7859 (t70) REVERT: C 252 MET cc_start: 0.7613 (mmm) cc_final: 0.6955 (mmt) REVERT: C 273 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7688 (tmm) REVERT: D 96 ARG cc_start: 0.9070 (ttt-90) cc_final: 0.8736 (ttt-90) REVERT: E 182 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8261 (tm) REVERT: E 260 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8245 (ptmt) REVERT: F 194 THR cc_start: 0.8759 (m) cc_final: 0.8424 (p) REVERT: G 77 ARG cc_start: 0.5451 (mtt180) cc_final: 0.5229 (mtp180) REVERT: G 236 ARG cc_start: 0.8399 (ttm170) cc_final: 0.7849 (mtt180) REVERT: G 253 ILE cc_start: 0.8246 (mt) cc_final: 0.7798 (tp) REVERT: H 99 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7170 (tp30) REVERT: H 155 SER cc_start: 0.9054 (t) cc_final: 0.8826 (p) REVERT: I 16 ASN cc_start: 0.8314 (m-40) cc_final: 0.6955 (p0) REVERT: J 16 VAL cc_start: 0.9522 (OUTLIER) cc_final: 0.9271 (m) REVERT: J 110 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8492 (tpp80) REVERT: J 156 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.8110 (t80) REVERT: J 245 THR cc_start: 0.7874 (p) cc_final: 0.7437 (t) REVERT: J 259 LEU cc_start: 0.9102 (mm) cc_final: 0.8899 (mp) REVERT: J 285 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.5937 (ptt180) REVERT: J 290 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: J 451 PHE cc_start: 0.8438 (m-10) cc_final: 0.8053 (m-10) REVERT: J 491 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5575 (p-80) REVERT: J 545 SER cc_start: 0.8952 (t) cc_final: 0.8456 (p) REVERT: J 623 ARG cc_start: 0.7302 (mtp180) cc_final: 0.6730 (mtp180) REVERT: J 667 MET cc_start: 0.9144 (mmm) cc_final: 0.8931 (mmm) REVERT: J 748 MET cc_start: 0.6191 (mmm) cc_final: 0.5657 (mmm) REVERT: J 826 TYR cc_start: 0.8476 (m-80) cc_final: 0.8263 (m-80) REVERT: J 919 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8069 (mm-40) outliers start: 104 outliers final: 69 residues processed: 620 average time/residue: 0.1469 time to fit residues: 144.4586 Evaluate side-chains 605 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 524 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 252 TYR Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 285 ARG Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 491 HIS Chi-restraints excluded: chain J residue 513 ILE Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 560 PHE Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 913 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 0.0040 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 GLN B 116 HIS C 162 ASN E 285 GLN G 88 HIS J 176 ASN J 920 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.176088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.146791 restraints weight = 31174.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.147464 restraints weight = 20796.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148893 restraints weight = 15503.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149748 restraints weight = 11751.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149689 restraints weight = 10922.552| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22503 Z= 0.116 Angle : 0.597 14.363 30573 Z= 0.295 Chirality : 0.042 0.272 3627 Planarity : 0.003 0.053 3956 Dihedral : 5.990 179.641 3261 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 5.03 % Allowed : 22.20 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2929 helix: 2.09 (0.18), residues: 856 sheet: 0.35 (0.22), residues: 579 loop : -1.26 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 92 TYR 0.013 0.001 TYR H 252 PHE 0.018 0.001 PHE C 154 TRP 0.009 0.001 TRP J 155 HIS 0.005 0.001 HIS G 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (22503) covalent geometry : angle 0.59691 / 0.29 (30573) hydrogen bonds : bond 0.03427 / 2.26 ( 995) hydrogen bonds : angle 4.16545 / 2.95 ( 2871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 537 time to evaluate : 0.845 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8541 (pttm) REVERT: A 98 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9071 (tt) REVERT: A 103 ASN cc_start: 0.9050 (t0) cc_final: 0.8695 (t0) REVERT: A 108 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8375 (ttm170) REVERT: A 190 MET cc_start: 0.8695 (mtm) cc_final: 0.8330 (mtt) REVERT: A 217 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8700 (ptt) REVERT: A 277 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7584 (pttp) REVERT: A 281 LYS cc_start: 0.7602 (mmmt) cc_final: 0.7073 (mptt) REVERT: B 26 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: C 60 CYS cc_start: 0.8182 (t) cc_final: 0.7777 (t) REVERT: C 75 ASP cc_start: 0.7835 (p0) cc_final: 0.7500 (t0) REVERT: C 83 VAL cc_start: 0.9250 (t) cc_final: 0.8961 (p) REVERT: C 115 ASN cc_start: 0.8627 (m-40) cc_final: 0.8398 (m-40) REVERT: C 122 GLU cc_start: 0.8064 (mp0) cc_final: 0.7767 (mp0) REVERT: C 191 THR cc_start: 0.8735 (p) cc_final: 0.8214 (t) REVERT: C 227 ASP cc_start: 0.8180 (m-30) cc_final: 0.7947 (m-30) REVERT: C 236 HIS cc_start: 0.8249 (t70) cc_final: 0.7848 (t70) REVERT: C 252 MET cc_start: 0.7660 (mmm) cc_final: 0.6946 (mmt) REVERT: C 265 LEU cc_start: 0.9023 (tt) cc_final: 0.8775 (tp) REVERT: C 266 MET cc_start: 0.7775 (tpp) cc_final: 0.7403 (tpp) REVERT: C 273 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7771 (tmm) REVERT: C 274 LYS cc_start: 0.8470 (mmmt) cc_final: 0.7575 (mmmt) REVERT: D 96 ARG cc_start: 0.9072 (ttt-90) cc_final: 0.8740 (ttt-90) REVERT: E 144 CYS cc_start: 0.8494 (t) cc_final: 0.8231 (m) REVERT: E 182 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8296 (tm) REVERT: E 260 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8208 (ptmt) REVERT: F 194 THR cc_start: 0.8706 (m) cc_final: 0.8374 (p) REVERT: F 206 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7821 (mtm110) REVERT: G 77 ARG cc_start: 0.5445 (mtt180) cc_final: 0.5232 (mtp180) REVERT: G 236 ARG cc_start: 0.8458 (ttm170) cc_final: 0.7677 (mtt180) REVERT: G 253 ILE cc_start: 0.8312 (mt) cc_final: 0.7799 (tp) REVERT: H 99 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7246 (tp30) REVERT: H 155 SER cc_start: 0.9059 (t) cc_final: 0.8858 (p) REVERT: H 197 LEU cc_start: 0.8904 (mm) cc_final: 0.8546 (mt) REVERT: H 234 ILE cc_start: 0.9457 (mt) cc_final: 0.9223 (mt) REVERT: I 16 ASN cc_start: 0.8343 (m-40) cc_final: 0.7082 (p0) REVERT: I 57 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7330 (mtp85) REVERT: J 16 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9284 (m) REVERT: J 110 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8493 (tpp80) REVERT: J 156 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.7929 (t80) REVERT: J 245 THR cc_start: 0.7886 (p) cc_final: 0.7449 (t) REVERT: J 259 LEU cc_start: 0.9101 (mm) cc_final: 0.8865 (mp) REVERT: J 290 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: J 451 PHE cc_start: 0.8241 (m-10) cc_final: 0.7857 (m-10) REVERT: J 545 SER cc_start: 0.8996 (t) cc_final: 0.8539 (p) REVERT: J 623 ARG cc_start: 0.7334 (mtp180) cc_final: 0.6623 (mtp180) REVERT: J 667 MET cc_start: 0.9141 (mmm) cc_final: 0.8917 (mmm) REVERT: J 682 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: J 826 TYR cc_start: 0.8457 (m-10) cc_final: 0.8257 (m-80) REVERT: J 919 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8016 (mm-40) outliers start: 113 outliers final: 75 residues processed: 609 average time/residue: 0.1444 time to fit residues: 139.7216 Evaluate side-chains 603 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 516 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 252 TYR Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 560 PHE Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 913 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 267 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 25 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 188 HIS ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN J 920 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143374 restraints weight = 31125.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144279 restraints weight = 20571.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145367 restraints weight = 15682.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147096 restraints weight = 12603.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.147196 restraints weight = 10396.609| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22503 Z= 0.146 Angle : 0.625 14.520 30573 Z= 0.310 Chirality : 0.044 0.256 3627 Planarity : 0.004 0.056 3956 Dihedral : 6.058 178.769 3261 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.50 % Rotamer: Outliers : 4.72 % Allowed : 22.51 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2929 helix: 2.12 (0.18), residues: 856 sheet: 0.23 (0.21), residues: 588 loop : -1.26 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 92 TYR 0.015 0.001 TYR H 252 PHE 0.018 0.001 PHE E 93 TRP 0.010 0.001 TRP J 155 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (22503) covalent geometry : angle 0.62472 / 0.31 (30573) hydrogen bonds : bond 0.03664 / 2.41 ( 995) hydrogen bonds : angle 4.22894 / 2.99 ( 2871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 545 time to evaluate : 0.840 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8549 (pttm) REVERT: A 98 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9036 (tt) REVERT: A 103 ASN cc_start: 0.9072 (t0) cc_final: 0.8740 (t0) REVERT: A 108 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8396 (ttm170) REVERT: A 190 MET cc_start: 0.8730 (mtm) cc_final: 0.8367 (mtt) REVERT: A 210 ASN cc_start: 0.8654 (p0) cc_final: 0.8063 (p0) REVERT: A 277 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7649 (pttp) REVERT: A 281 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7194 (mptt) REVERT: B 26 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: B 155 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: C 60 CYS cc_start: 0.8100 (t) cc_final: 0.7795 (t) REVERT: C 75 ASP cc_start: 0.7875 (p0) cc_final: 0.7478 (t0) REVERT: C 83 VAL cc_start: 0.9281 (t) cc_final: 0.8995 (p) REVERT: C 115 ASN cc_start: 0.8521 (m-40) cc_final: 0.8231 (m-40) REVERT: C 122 GLU cc_start: 0.8067 (mp0) cc_final: 0.7781 (mp0) REVERT: C 191 THR cc_start: 0.8596 (p) cc_final: 0.8182 (t) REVERT: C 252 MET cc_start: 0.7663 (mmm) cc_final: 0.7000 (mmt) REVERT: C 273 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7934 (tmm) REVERT: D 96 ARG cc_start: 0.9033 (ttt-90) cc_final: 0.8720 (ttt-90) REVERT: E 44 ASN cc_start: 0.8714 (t0) cc_final: 0.8498 (t0) REVERT: E 144 CYS cc_start: 0.8492 (t) cc_final: 0.8276 (m) REVERT: E 182 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8579 (tm) REVERT: F 194 THR cc_start: 0.8719 (m) cc_final: 0.8340 (p) REVERT: F 206 ARG cc_start: 0.8278 (mmt-90) cc_final: 0.7943 (mtm110) REVERT: G 113 LYS cc_start: 0.6891 (tttp) cc_final: 0.6540 (tttp) REVERT: G 151 LYS cc_start: 0.7019 (ttpp) cc_final: 0.5931 (mtmt) REVERT: G 236 ARG cc_start: 0.8594 (ttm170) cc_final: 0.7515 (mtt180) REVERT: G 253 ILE cc_start: 0.8358 (mt) cc_final: 0.7899 (tp) REVERT: H 47 MET cc_start: 0.8539 (mmm) cc_final: 0.8248 (mmm) REVERT: H 99 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7285 (tp30) REVERT: H 291 GLN cc_start: 0.7769 (tp-100) cc_final: 0.6924 (tp40) REVERT: I 16 ASN cc_start: 0.8001 (m-40) cc_final: 0.6843 (p0) REVERT: I 57 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7241 (mtp85) REVERT: J 16 VAL cc_start: 0.9579 (OUTLIER) cc_final: 0.9336 (m) REVERT: J 110 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8482 (tpp80) REVERT: J 156 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8273 (t80) REVERT: J 245 THR cc_start: 0.7885 (p) cc_final: 0.7428 (t) REVERT: J 259 LEU cc_start: 0.9096 (mm) cc_final: 0.8851 (mp) REVERT: J 290 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: J 433 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8637 (tp) REVERT: J 451 PHE cc_start: 0.8243 (m-10) cc_final: 0.7880 (m-10) REVERT: J 491 HIS cc_start: 0.5994 (OUTLIER) cc_final: 0.5435 (p-80) REVERT: J 531 TYR cc_start: 0.8371 (m-80) cc_final: 0.8078 (m-80) REVERT: J 545 SER cc_start: 0.8999 (t) cc_final: 0.8572 (p) REVERT: J 623 ARG cc_start: 0.7366 (mtp180) cc_final: 0.6788 (mtp180) REVERT: J 667 MET cc_start: 0.9136 (mmm) cc_final: 0.8915 (mmm) REVERT: J 682 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.5886 (m-80) outliers start: 106 outliers final: 77 residues processed: 610 average time/residue: 0.1487 time to fit residues: 143.0807 Evaluate side-chains 612 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 522 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 252 TYR Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 491 HIS Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 560 PHE Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 913 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 249 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 112 ASN A 235 GLN C 162 ASN H 199 ASN J 920 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.173315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.143523 restraints weight = 31187.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.145111 restraints weight = 19393.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.146396 restraints weight = 13860.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147022 restraints weight = 11101.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147263 restraints weight = 9738.267| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22503 Z= 0.130 Angle : 0.630 15.313 30573 Z= 0.312 Chirality : 0.043 0.264 3627 Planarity : 0.004 0.054 3956 Dihedral : 6.050 177.588 3261 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 4.67 % Allowed : 23.18 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2929 helix: 2.11 (0.18), residues: 857 sheet: 0.17 (0.21), residues: 598 loop : -1.22 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 924 TYR 0.013 0.001 TYR H 252 PHE 0.016 0.001 PHE E 93 TRP 0.010 0.001 TRP J 155 HIS 0.007 0.001 HIS J 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (22503) covalent geometry : angle 0.62996 / 0.31 (30573) hydrogen bonds : bond 0.03581 / 2.36 ( 995) hydrogen bonds : angle 4.19980 / 2.98 ( 2871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 538 time to evaluate : 0.808 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8619 (pttm) REVERT: A 98 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8999 (tt) REVERT: A 103 ASN cc_start: 0.9054 (t0) cc_final: 0.8710 (t0) REVERT: A 108 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8407 (ttm170) REVERT: A 112 ASN cc_start: 0.9158 (m-40) cc_final: 0.8829 (m110) REVERT: A 190 MET cc_start: 0.8771 (mtm) cc_final: 0.8309 (mtt) REVERT: A 277 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7608 (pttp) REVERT: A 281 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7094 (mptt) REVERT: B 26 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: B 95 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8106 (mtpt) REVERT: C 60 CYS cc_start: 0.8121 (t) cc_final: 0.7813 (t) REVERT: C 83 VAL cc_start: 0.9296 (t) cc_final: 0.8989 (p) REVERT: C 115 ASN cc_start: 0.8524 (m-40) cc_final: 0.8170 (m-40) REVERT: C 122 GLU cc_start: 0.8183 (mp0) cc_final: 0.7921 (mp0) REVERT: C 191 THR cc_start: 0.8587 (p) cc_final: 0.8171 (t) REVERT: C 252 MET cc_start: 0.7702 (mmm) cc_final: 0.7081 (mmt) REVERT: C 273 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7903 (tmm) REVERT: C 274 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7442 (mmmt) REVERT: D 96 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8718 (ttt-90) REVERT: E 44 ASN cc_start: 0.8813 (t0) cc_final: 0.8559 (t0) REVERT: E 144 CYS cc_start: 0.8517 (t) cc_final: 0.8279 (m) REVERT: E 182 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8447 (tm) REVERT: F 194 THR cc_start: 0.8669 (m) cc_final: 0.8305 (p) REVERT: G 113 LYS cc_start: 0.6839 (tttp) cc_final: 0.6482 (tttp) REVERT: G 151 LYS cc_start: 0.7040 (ttpp) cc_final: 0.5957 (mttm) REVERT: G 236 ARG cc_start: 0.8509 (ttm170) cc_final: 0.7738 (mtt180) REVERT: G 253 ILE cc_start: 0.8305 (mt) cc_final: 0.7887 (tp) REVERT: H 47 MET cc_start: 0.8562 (mmm) cc_final: 0.8286 (mmm) REVERT: H 99 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7234 (tp30) REVERT: H 291 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7095 (tp40) REVERT: I 16 ASN cc_start: 0.8013 (m-40) cc_final: 0.6798 (p0) REVERT: I 57 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7135 (mtp85) REVERT: J 110 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8490 (tpp80) REVERT: J 156 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8353 (t80) REVERT: J 245 THR cc_start: 0.7848 (p) cc_final: 0.7373 (t) REVERT: J 259 LEU cc_start: 0.9115 (mm) cc_final: 0.8874 (mp) REVERT: J 433 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8696 (tp) REVERT: J 434 LEU cc_start: 0.9259 (tp) cc_final: 0.8952 (tp) REVERT: J 451 PHE cc_start: 0.8287 (m-10) cc_final: 0.7936 (m-10) REVERT: J 491 HIS cc_start: 0.5928 (OUTLIER) cc_final: 0.5350 (p-80) REVERT: J 531 TYR cc_start: 0.8347 (m-80) cc_final: 0.8087 (m-80) REVERT: J 545 SER cc_start: 0.8994 (t) cc_final: 0.8532 (p) REVERT: J 623 ARG cc_start: 0.7406 (mtp180) cc_final: 0.6858 (mtp180) REVERT: J 641 MET cc_start: 0.4024 (mpp) cc_final: 0.2971 (mmt) REVERT: J 667 MET cc_start: 0.9146 (mmm) cc_final: 0.8939 (mmm) REVERT: J 682 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5962 (m-80) outliers start: 105 outliers final: 84 residues processed: 601 average time/residue: 0.1494 time to fit residues: 141.2835 Evaluate side-chains 613 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 519 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 491 HIS Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 560 PHE Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 913 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 228 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 153 optimal weight: 0.3980 chunk 246 optimal weight: 6.9990 chunk 164 optimal weight: 0.0370 chunk 133 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 188 HIS A 235 GLN B 105 GLN H 199 ASN J 441 HIS J 920 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.174351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144099 restraints weight = 31493.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.145395 restraints weight = 19009.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146694 restraints weight = 14013.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.147952 restraints weight = 11367.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.148366 restraints weight = 9863.695| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22503 Z= 0.120 Angle : 0.629 15.306 30573 Z= 0.311 Chirality : 0.043 0.271 3627 Planarity : 0.004 0.050 3956 Dihedral : 5.998 176.773 3261 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.84 % Rotamer: Outliers : 4.14 % Allowed : 24.15 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2929 helix: 2.12 (0.18), residues: 858 sheet: 0.17 (0.21), residues: 608 loop : -1.18 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 924 TYR 0.021 0.001 TYR J 531 PHE 0.014 0.001 PHE E 93 TRP 0.010 0.001 TRP J 564 HIS 0.010 0.001 HIS J 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (22503) covalent geometry : angle 0.62949 / 0.31 (30573) hydrogen bonds : bond 0.03464 / 2.29 ( 995) hydrogen bonds : angle 4.14729 / 2.94 ( 2871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 531 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8638 (pttm) REVERT: A 98 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9017 (tt) REVERT: A 103 ASN cc_start: 0.9042 (t0) cc_final: 0.8720 (t0) REVERT: A 108 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8462 (ttm170) REVERT: A 190 MET cc_start: 0.8719 (mtm) cc_final: 0.8237 (mtt) REVERT: A 277 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7622 (pttp) REVERT: A 281 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7178 (mptt) REVERT: B 26 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: B 95 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8064 (mtpt) REVERT: C 60 CYS cc_start: 0.8037 (t) cc_final: 0.7714 (t) REVERT: C 83 VAL cc_start: 0.9269 (t) cc_final: 0.8969 (p) REVERT: C 115 ASN cc_start: 0.8477 (m-40) cc_final: 0.8271 (m-40) REVERT: C 122 GLU cc_start: 0.8127 (mp0) cc_final: 0.7850 (mp0) REVERT: C 191 THR cc_start: 0.8601 (p) cc_final: 0.8191 (t) REVERT: C 252 MET cc_start: 0.7537 (mmm) cc_final: 0.6968 (mmt) REVERT: C 266 MET cc_start: 0.8736 (tpt) cc_final: 0.8338 (tpp) REVERT: C 273 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7944 (tmm) REVERT: D 96 ARG cc_start: 0.9017 (ttt-90) cc_final: 0.8714 (ttt-90) REVERT: D 193 LEU cc_start: 0.9369 (mt) cc_final: 0.9084 (mt) REVERT: E 144 CYS cc_start: 0.8308 (t) cc_final: 0.8107 (m) REVERT: E 182 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8579 (tm) REVERT: F 194 THR cc_start: 0.8658 (m) cc_final: 0.8313 (p) REVERT: G 113 LYS cc_start: 0.6872 (tttp) cc_final: 0.6496 (tttp) REVERT: G 124 LYS cc_start: 0.6445 (ttpt) cc_final: 0.5900 (tttm) REVERT: G 151 LYS cc_start: 0.6988 (ttpp) cc_final: 0.5936 (mttm) REVERT: G 236 ARG cc_start: 0.8449 (ttm170) cc_final: 0.7793 (mtt180) REVERT: G 253 ILE cc_start: 0.8357 (mt) cc_final: 0.7946 (tp) REVERT: H 47 MET cc_start: 0.8548 (mmm) cc_final: 0.8277 (mmm) REVERT: H 65 LYS cc_start: 0.5463 (mmmt) cc_final: 0.5179 (ptpp) REVERT: H 99 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7278 (tp30) REVERT: H 291 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7099 (tp40) REVERT: I 16 ASN cc_start: 0.8002 (m-40) cc_final: 0.6825 (p0) REVERT: I 57 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7125 (mtp85) REVERT: J 16 VAL cc_start: 0.9588 (OUTLIER) cc_final: 0.9346 (m) REVERT: J 110 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8471 (tpp80) REVERT: J 156 TYR cc_start: 0.9352 (OUTLIER) cc_final: 0.8333 (t80) REVERT: J 245 THR cc_start: 0.7810 (p) cc_final: 0.7349 (t) REVERT: J 259 LEU cc_start: 0.9063 (mm) cc_final: 0.8817 (mp) REVERT: J 285 ARG cc_start: 0.8807 (mpt180) cc_final: 0.8600 (mmt180) REVERT: J 433 LEU cc_start: 0.9142 (pp) cc_final: 0.8796 (tp) REVERT: J 434 LEU cc_start: 0.9240 (tp) cc_final: 0.8942 (tp) REVERT: J 451 PHE cc_start: 0.8235 (m-10) cc_final: 0.7936 (m-10) REVERT: J 491 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.5058 (p-80) REVERT: J 500 LEU cc_start: 0.6149 (mm) cc_final: 0.5924 (mp) REVERT: J 531 TYR cc_start: 0.8447 (m-80) cc_final: 0.8147 (m-80) REVERT: J 545 SER cc_start: 0.8970 (t) cc_final: 0.8576 (p) REVERT: J 551 LEU cc_start: 0.7046 (mt) cc_final: 0.6835 (mt) REVERT: J 623 ARG cc_start: 0.7385 (mtp180) cc_final: 0.6836 (mtp180) REVERT: J 641 MET cc_start: 0.4040 (mpp) cc_final: 0.2947 (mmt) REVERT: J 667 MET cc_start: 0.9152 (mmm) cc_final: 0.8927 (mmm) REVERT: J 671 ASN cc_start: 0.7873 (m-40) cc_final: 0.7387 (m-40) REVERT: J 682 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5879 (m-80) outliers start: 93 outliers final: 75 residues processed: 588 average time/residue: 0.1500 time to fit residues: 139.0915 Evaluate side-chains 611 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 526 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 491 HIS Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 560 PHE Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 620 LEU Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 913 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 82 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 289 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 291 optimal weight: 0.0040 chunk 211 optimal weight: 0.9990 chunk 244 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 186 optimal weight: 0.4980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 235 GLN H 199 ASN J 920 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.171594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141278 restraints weight = 31405.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143460 restraints weight = 18964.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.144429 restraints weight = 12895.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.144993 restraints weight = 10382.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.145455 restraints weight = 9255.052| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22503 Z= 0.121 Angle : 0.628 15.717 30573 Z= 0.311 Chirality : 0.043 0.269 3627 Planarity : 0.004 0.050 3956 Dihedral : 5.991 176.206 3261 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 4.23 % Allowed : 24.02 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2929 helix: 2.14 (0.18), residues: 856 sheet: 0.18 (0.21), residues: 608 loop : -1.17 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 924 TYR 0.022 0.001 TYR J 121 PHE 0.015 0.001 PHE E 93 TRP 0.010 0.001 TRP J 564 HIS 0.007 0.001 HIS J 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22503) covalent geometry : angle 0.62753 / 0.31 (30573) hydrogen bonds : bond 0.03458 / 2.29 ( 995) hydrogen bonds : angle 4.13854 / 2.93 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.29 seconds wall clock time: 71 minutes 15.72 seconds (4275.72 seconds total)