Starting phenix.real_space_refine on Thu Nov 20 11:36:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rer_4854/11_2025/6rer_4854.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rer_4854/11_2025/6rer_4854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rer_4854/11_2025/6rer_4854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rer_4854/11_2025/6rer_4854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rer_4854/11_2025/6rer_4854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rer_4854/11_2025/6rer_4854.map" } resolution = 2.9 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= 0.005 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21545 2.51 5 N 5796 2.21 5 O 6424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 242 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33899 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.70, per 1000 atoms: 0.23 Number of scatterers: 33899 At special positions: 0 Unit cell: (163.215, 134.784, 206.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6424 8.00 N 5796 7.00 C 21545 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: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 53.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 54 through 67 removed outlier: 4.056A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.290A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.600A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.009A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.638A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.113A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.641A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.053A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.942A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.586A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 4.611A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.452A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 removed outlier: 3.651A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 127 removed outlier: 4.106A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.749A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.387A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.632A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.013A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.260A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 111 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.589A pdb=" N SER G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.822A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.358A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 4.048A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.894A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 92 removed outlier: 3.601A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 97 through 124 removed outlier: 3.505A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.804A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.174A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 96 removed outlier: 3.679A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 96' Processing helix chain 'J' and resid 97 through 126 removed outlier: 3.783A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 64 removed outlier: 3.583A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU P 64 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.935A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 115 through 126 removed outlier: 3.758A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 4.117A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'R' and resid 29 through 41 removed outlier: 4.148A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 54 Processing helix chain 'R' and resid 157 through 169 removed outlier: 4.400A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA R 169 " --> pdb=" O ALA R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 removed outlier: 4.107A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.672A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.465A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 130 removed outlier: 3.760A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR S 130 " --> pdb=" O THR S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 151 removed outlier: 3.911A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 212 through 217 Processing helix chain 'S' and resid 227 through 231 removed outlier: 3.758A pdb=" N ALA S 230 " --> pdb=" O SER S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 315 removed outlier: 3.753A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.912A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 246 Processing helix chain 'T' and resid 267 through 280 removed outlier: 3.585A pdb=" N VAL T 273 " --> pdb=" O VAL T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.155A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 341 Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 353 through 363 Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.574A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS T 415 " --> pdb=" O GLU T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.678A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.664A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 457 removed outlier: 3.621A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 removed outlier: 4.103A pdb=" N GLN T 461 " --> pdb=" O ALA T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.539A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.660A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS T 506 " --> pdb=" O TYR T 502 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.589A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 546 through 556 Processing helix chain 'U' and resid 41 through 48 removed outlier: 3.604A pdb=" N LEU U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 71 removed outlier: 4.459A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 72 through 74 No H-bonds generated for 'chain 'U' and resid 72 through 74' Processing helix chain 'U' and resid 134 through 138 removed outlier: 4.101A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.559A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.836A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.544A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.787A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 340 removed outlier: 3.661A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.758A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 414 removed outlier: 3.651A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 455 removed outlier: 3.560A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.700A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 468 Processing helix chain 'U' and resid 469 through 484 removed outlier: 3.677A pdb=" N LEU U 474 " --> pdb=" O THR U 470 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 removed outlier: 3.604A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 506 removed outlier: 3.536A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.938A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.779A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 545 through 554 removed outlier: 3.628A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 removed outlier: 3.521A pdb=" N LEU V 48 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 45 through 49' Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.888A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.825A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.688A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.929A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 removed outlier: 3.670A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 280 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 4.265A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.595A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.688A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.848A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 415 removed outlier: 3.548A pdb=" N PHE V 413 " --> pdb=" O GLU V 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 454 removed outlier: 4.087A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 485 removed outlier: 3.767A pdb=" N LEU V 474 " --> pdb=" O THR V 470 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU V 484 " --> pdb=" O LEU V 480 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 507 removed outlier: 3.775A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY V 507 " --> pdb=" O ALA V 503 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.618A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.560A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 554 removed outlier: 4.338A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 201 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.857A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 Processing helix chain 'X' and resid 260 through 275 Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.900A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER X 298 " --> pdb=" O ASN X 294 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.629A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 395 through 418 removed outlier: 4.419A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 444 removed outlier: 3.671A pdb=" N ALA X 434 " --> pdb=" O LYS X 430 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER X 444 " --> pdb=" O GLN X 440 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 removed outlier: 3.534A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 487 removed outlier: 3.629A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 507 removed outlier: 3.769A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 removed outlier: 3.629A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 149 through 153 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 204 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 237 through 242 removed outlier: 4.186A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 4.838A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 removed outlier: 3.536A pdb=" N PHE Y 290 " --> pdb=" O ASN Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.817A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 365 through 370 Processing helix chain 'Y' and resid 392 through 412 removed outlier: 4.282A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 430 through 443 removed outlier: 4.095A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 447 through 449 No H-bonds generated for 'chain 'Y' and resid 447 through 449' Processing helix chain 'Y' and resid 450 through 455 removed outlier: 3.527A pdb=" N GLY Y 455 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.912A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 494 through 503 Processing helix chain 'Y' and resid 505 through 510 removed outlier: 3.848A pdb=" N ARG Y 509 " --> pdb=" O ASP Y 505 " (cutoff:3.500A) Processing helix chain 'Y' and resid 518 through 523 removed outlier: 4.148A pdb=" N LYS Y 522 " --> pdb=" O SER Y 518 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP Y 523 " --> pdb=" O GLU Y 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 518 through 523' Processing helix chain 'Y' and resid 526 through 532 removed outlier: 3.552A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER Y 532 " --> pdb=" O ASP Y 528 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 554 removed outlier: 4.081A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.605A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 204 removed outlier: 4.543A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.994A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.643A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.938A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 371 Processing helix chain 'Z' and resid 393 through 413 removed outlier: 3.506A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 3.530A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 422 through 425 Processing helix chain 'Z' and resid 426 through 443 removed outlier: 3.706A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 491 through 508 removed outlier: 3.702A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.679A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) 1441 hydrogen bonds defined for protein. 4182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10763 1.34 - 1.45: 4548 1.45 - 1.57: 18888 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 46332 3.68 - 7.37: 275 7.37 - 11.05: 31 11.05 - 14.73: 7 14.73 - 18.42: 4 Bond angle restraints: 46649 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.45 18.42 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 122.40 17.47 1.00e+00 1.00e+00 3.05e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.52 17.35 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.20 14.63 1.00e+00 1.00e+00 2.14e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 20289 31.89 - 63.78: 487 63.78 - 95.67: 47 95.67 - 127.56: 1 127.56 - 159.45: 4 Dihedral angle restraints: 20828 sinusoidal: 8068 harmonic: 12760 Sorted by residual: dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -126.90 -53.10 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -128.27 -51.73 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -128.91 -51.09 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 20825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4307 0.061 - 0.123: 1046 0.123 - 0.184: 152 0.184 - 0.246: 10 0.246 - 0.307: 5 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB ILE H 95 " pdb=" CA ILE H 95 " pdb=" CG1 ILE H 95 " pdb=" CG2 ILE H 95 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE S 183 " pdb=" CA ILE S 183 " pdb=" CG1 ILE S 183 " pdb=" CG2 ILE S 183 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.033 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" C ALA X 503 " 0.110 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.06e-02 3.67e+01 pdb=" C ALA Z 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP Y 348 " -0.047 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO Y 349 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO Y 349 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO Y 349 " -0.040 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4952 2.76 - 3.29: 32082 3.29 - 3.83: 59649 3.83 - 4.36: 73241 4.36 - 4.90: 122651 Nonbonded interactions: 292575 Sorted by model distance: nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.219 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.225 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.230 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.241 2.170 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.253 2.170 ... (remaining 292570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } 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 individual isotropic 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: 10.320 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 31.560 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 0.083 34420 Z= 0.289 Angle : 0.881 18.419 46649 Z= 0.517 Chirality : 0.054 0.307 5520 Planarity : 0.007 0.072 5999 Dihedral : 14.408 159.451 12666 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.10), residues: 4462 helix: -2.94 (0.08), residues: 2134 sheet: -1.37 (0.22), residues: 485 loop : -1.88 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 217 TYR 0.017 0.002 TYR U 57 PHE 0.028 0.002 PHE A 122 TRP 0.021 0.002 TRP Z 141 HIS 0.008 0.001 HIS R 104 Details of bonding type rmsd covalent geometry : bond 0.00603 (34420) covalent geometry : angle 0.88062 (46649) hydrogen bonds : bond 0.16266 ( 1441) hydrogen bonds : angle 7.00970 ( 4182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 711 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8330 (t0) cc_final: 0.8052 (t0) REVERT: E 91 ARG cc_start: 0.7714 (mtt-85) cc_final: 0.7411 (mtm180) REVERT: E 95 ILE cc_start: 0.8132 (pt) cc_final: 0.7860 (pt) REVERT: E 119 LEU cc_start: 0.6988 (tp) cc_final: 0.6647 (mt) REVERT: G 102 TYR cc_start: 0.6903 (m-10) cc_final: 0.6684 (m-80) REVERT: P 66 GLN cc_start: 0.7215 (tt0) cc_final: 0.6951 (mm-40) REVERT: P 145 MET cc_start: 0.8939 (mmm) cc_final: 0.8565 (mmm) REVERT: Q 43 GLN cc_start: 0.8701 (tt0) cc_final: 0.8491 (tt0) REVERT: R 110 GLN cc_start: 0.8662 (tt0) cc_final: 0.8326 (tt0) REVERT: R 115 VAL cc_start: 0.8697 (p) cc_final: 0.8446 (t) REVERT: S 188 GLN cc_start: 0.7785 (mt0) cc_final: 0.7189 (mp10) REVERT: S 219 GLN cc_start: 0.7884 (mt0) cc_final: 0.7659 (mt0) REVERT: S 248 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7263 (mt-10) REVERT: S 261 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7961 (mm-30) REVERT: S 271 MET cc_start: 0.8429 (ttp) cc_final: 0.8181 (ttp) REVERT: T 530 PRO cc_start: 0.8170 (Cg_exo) cc_final: 0.7827 (Cg_endo) REVERT: U 50 LYS cc_start: 0.6508 (mppt) cc_final: 0.6249 (mptt) REVERT: U 337 MET cc_start: 0.8527 (ttp) cc_final: 0.8242 (ttp) REVERT: U 471 GLN cc_start: 0.7357 (tp-100) cc_final: 0.6947 (tm-30) REVERT: U 474 LEU cc_start: 0.7207 (pp) cc_final: 0.6809 (pp) REVERT: U 487 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7588 (mmtm) REVERT: U 502 TYR cc_start: 0.7949 (t80) cc_final: 0.7700 (t80) REVERT: U 537 LYS cc_start: 0.8112 (tptt) cc_final: 0.7839 (tptp) REVERT: U 551 LYS cc_start: 0.7715 (mttt) cc_final: 0.7452 (mtpt) REVERT: U 559 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6597 (pp) REVERT: V 65 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7929 (mmtt) REVERT: V 467 ASP cc_start: 0.6090 (m-30) cc_final: 0.5700 (t0) REVERT: X 502 MET cc_start: 0.7670 (mtp) cc_final: 0.7451 (mtm) REVERT: Y 493 LYS cc_start: 0.8076 (tmmt) cc_final: 0.7660 (tmtm) REVERT: Z 82 ASP cc_start: 0.7530 (t0) cc_final: 0.7233 (t0) REVERT: Z 386 MET cc_start: 0.8185 (mmm) cc_final: 0.7882 (mmm) REVERT: Z 502 MET cc_start: 0.7829 (mtp) cc_final: 0.7550 (mtm) outliers start: 6 outliers final: 1 residues processed: 713 average time/residue: 0.7325 time to fit residues: 621.5838 Evaluate side-chains 401 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain U residue 559 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN J 87 ASN P 52 GLN R 38 ASN R 53 ASN R 73 ASN R 85 GLN R 137 HIS S 98 ASN S 174 GLN T 134 ASN T 241 HIS T 253 GLN T 358 HIS T 386 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN U 60 GLN U 78 GLN U 83 HIS U 196 GLN U 242 GLN U 319 HIS U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN V 64 GLN V 123 GLN V 126 HIS V 134 ASN V 139 HIS V 152 ASN V 241 HIS V 242 GLN V 244 ASN V 435 GLN V 441 GLN V 486 GLN V 497 GLN X 157 GLN X 204 HIS X 278 GLN Y 157 GLN Y 199 ASN Y 278 GLN Y 294 ASN Y 322 GLN Y 337 GLN Y 440 GLN Z 42 GLN Z 83 ASN Z 199 ASN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107396 restraints weight = 49524.825| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.81 r_work: 0.3210 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34420 Z= 0.129 Angle : 0.568 9.657 46649 Z= 0.291 Chirality : 0.043 0.269 5520 Planarity : 0.005 0.056 5999 Dihedral : 7.602 149.668 4923 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.16 % Favored : 96.66 % Rotamer: Outliers : 2.83 % Allowed : 13.41 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.95 (0.12), residues: 4462 helix: -1.14 (0.10), residues: 2185 sheet: -1.15 (0.21), residues: 534 loop : -1.30 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 124 TYR 0.018 0.001 TYR Z 248 PHE 0.024 0.001 PHE A 122 TRP 0.008 0.001 TRP Z 141 HIS 0.004 0.001 HIS V 61 Details of bonding type rmsd covalent geometry : bond 0.00287 (34420) covalent geometry : angle 0.56818 (46649) hydrogen bonds : bond 0.03913 ( 1441) hydrogen bonds : angle 4.64152 ( 4182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 486 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8505 (t0) cc_final: 0.8080 (t0) REVERT: A 95 ILE cc_start: 0.7409 (pt) cc_final: 0.7168 (mp) REVERT: B 81 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7920 (ptp) REVERT: C 102 TYR cc_start: 0.8286 (m-80) cc_final: 0.7912 (m-80) REVERT: E 91 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7769 (mtm180) REVERT: E 92 ASN cc_start: 0.8061 (t0) cc_final: 0.7782 (t0) REVERT: E 95 ILE cc_start: 0.8086 (pt) cc_final: 0.7850 (pp) REVERT: E 109 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7224 (tp) REVERT: E 119 LEU cc_start: 0.6791 (tp) cc_final: 0.6381 (mt) REVERT: G 98 GLN cc_start: 0.7260 (mm110) cc_final: 0.6491 (tt0) REVERT: I 115 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.5923 (pp) REVERT: P 79 GLU cc_start: 0.7782 (tp30) cc_final: 0.7523 (tp30) REVERT: P 145 MET cc_start: 0.9032 (mmm) cc_final: 0.8782 (mmm) REVERT: Q 38 LYS cc_start: 0.8212 (mttt) cc_final: 0.7745 (mmtm) REVERT: Q 48 ARG cc_start: 0.8278 (ptt-90) cc_final: 0.7800 (ptt180) REVERT: R 49 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7218 (mt-10) REVERT: R 54 TYR cc_start: 0.8200 (m-80) cc_final: 0.7816 (m-80) REVERT: R 110 GLN cc_start: 0.8927 (tt0) cc_final: 0.8599 (tt0) REVERT: R 171 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6112 (pp30) REVERT: R 175 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7052 (pm20) REVERT: R 176 PHE cc_start: 0.7797 (t80) cc_final: 0.7395 (t80) REVERT: R 196 GLU cc_start: 0.7061 (mp0) cc_final: 0.6323 (mm-30) REVERT: S 112 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8354 (m) REVERT: S 124 ARG cc_start: 0.7847 (ptm-80) cc_final: 0.7538 (ptm-80) REVERT: S 147 ARG cc_start: 0.7479 (ptt90) cc_final: 0.6599 (ptm-80) REVERT: S 248 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7959 (mt-10) REVERT: U 92 ASP cc_start: 0.8338 (m-30) cc_final: 0.8083 (m-30) REVERT: U 149 GLN cc_start: 0.8136 (mt0) cc_final: 0.7809 (mm110) REVERT: U 482 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: U 487 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7871 (mtpt) REVERT: U 537 LYS cc_start: 0.8094 (tptt) cc_final: 0.7784 (tptp) REVERT: U 551 LYS cc_start: 0.7654 (mttt) cc_final: 0.7241 (mtpt) REVERT: U 559 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6633 (pp) REVERT: V 467 ASP cc_start: 0.6155 (m-30) cc_final: 0.5585 (t0) REVERT: V 521 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7562 (tt0) REVERT: X 158 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: X 390 ASN cc_start: 0.8476 (m-40) cc_final: 0.8122 (t0) REVERT: Y 430 LYS cc_start: 0.6494 (ttmt) cc_final: 0.6188 (mtmt) REVERT: Y 494 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: Y 501 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6702 (tmtp) REVERT: Z 82 ASP cc_start: 0.8439 (t0) cc_final: 0.8007 (t0) REVERT: Z 371 LEU cc_start: 0.8782 (mp) cc_final: 0.8552 (mp) REVERT: Z 550 LYS cc_start: 0.6968 (tppt) cc_final: 0.6100 (tptp) outliers start: 101 outliers final: 25 residues processed: 549 average time/residue: 0.7273 time to fit residues: 480.0245 Evaluate side-chains 406 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain R residue 161 LYS Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 494 GLU Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 415 ASP Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 531 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 422 optimal weight: 0.0370 chunk 307 optimal weight: 4.9990 chunk 396 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 425 optimal weight: 0.7980 chunk 384 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN H 98 GLN I 94 ASN P 52 GLN P 83 GLN R 53 ASN T 441 GLN T 497 GLN U 60 GLN U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN V 134 ASN V 228 GLN ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN Y 83 ASN Y 440 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108095 restraints weight = 49442.676| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.91 r_work: 0.3202 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34420 Z= 0.132 Angle : 0.549 9.868 46649 Z= 0.279 Chirality : 0.043 0.258 5520 Planarity : 0.004 0.065 5999 Dihedral : 7.085 152.101 4921 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.95 % Allowed : 15.62 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.04 (0.12), residues: 4462 helix: -0.19 (0.11), residues: 2169 sheet: -1.03 (0.21), residues: 531 loop : -1.04 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 124 TYR 0.023 0.001 TYR P 75 PHE 0.022 0.001 PHE A 122 TRP 0.004 0.001 TRP Z 141 HIS 0.004 0.001 HIS S 250 Details of bonding type rmsd covalent geometry : bond 0.00299 (34420) covalent geometry : angle 0.54854 (46649) hydrogen bonds : bond 0.03702 ( 1441) hydrogen bonds : angle 4.28239 ( 4182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 458 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6087 (mt) cc_final: 0.5815 (tp) REVERT: A 92 ASN cc_start: 0.8429 (t0) cc_final: 0.8001 (t0) REVERT: D 113 ILE cc_start: 0.7506 (mt) cc_final: 0.7293 (mp) REVERT: E 71 LEU cc_start: 0.6624 (mm) cc_final: 0.6304 (mp) REVERT: E 91 ARG cc_start: 0.8239 (mtt-85) cc_final: 0.7861 (mtm180) REVERT: E 92 ASN cc_start: 0.8213 (t0) cc_final: 0.7936 (t0) REVERT: E 95 ILE cc_start: 0.8129 (pt) cc_final: 0.7801 (pt) REVERT: E 109 LEU cc_start: 0.7499 (tp) cc_final: 0.7188 (tp) REVERT: E 119 LEU cc_start: 0.6741 (tp) cc_final: 0.6364 (mt) REVERT: J 56 LEU cc_start: 0.5088 (tm) cc_final: 0.4680 (mm) REVERT: P 83 GLN cc_start: 0.8291 (mt0) cc_final: 0.7867 (mt0) REVERT: P 145 MET cc_start: 0.9033 (mmm) cc_final: 0.8815 (mmm) REVERT: Q 38 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7691 (mmtm) REVERT: Q 48 ARG cc_start: 0.8272 (ppt-90) cc_final: 0.7745 (ptt180) REVERT: R 110 GLN cc_start: 0.8960 (tt0) cc_final: 0.8623 (tt0) REVERT: R 171 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6165 (pp30) REVERT: S 147 ARG cc_start: 0.7589 (ptt90) cc_final: 0.6681 (ptm-80) REVERT: S 216 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7105 (mm) REVERT: S 248 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8141 (mt-10) REVERT: T 86 ARG cc_start: 0.8433 (mpp-170) cc_final: 0.8176 (mtt90) REVERT: T 456 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8311 (p) REVERT: U 149 GLN cc_start: 0.8191 (mt0) cc_final: 0.7792 (mm110) REVERT: U 199 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7313 (mtt90) REVERT: U 475 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: U 487 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7828 (mtpt) REVERT: U 511 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6057 (mtmt) REVERT: U 537 LYS cc_start: 0.8095 (tptt) cc_final: 0.7780 (tptp) REVERT: U 551 LYS cc_start: 0.7581 (mttt) cc_final: 0.7180 (mtpt) REVERT: U 559 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6693 (mt) REVERT: V 61 HIS cc_start: 0.8066 (m-70) cc_final: 0.7859 (m-70) REVERT: V 467 ASP cc_start: 0.6014 (m-30) cc_final: 0.5385 (t0) REVERT: V 521 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7560 (tt0) REVERT: X 101 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8682 (ttpp) REVERT: X 158 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: X 390 ASN cc_start: 0.8454 (m110) cc_final: 0.8155 (t0) REVERT: Y 344 ASP cc_start: 0.8102 (t0) cc_final: 0.7650 (t0) REVERT: Y 430 LYS cc_start: 0.6636 (ttmt) cc_final: 0.6298 (mtmt) REVERT: Y 488 MET cc_start: 0.7846 (mmm) cc_final: 0.7286 (mmt) REVERT: Y 501 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6647 (tmtp) REVERT: Z 51 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8299 (ttm110) REVERT: Z 82 ASP cc_start: 0.8404 (t0) cc_final: 0.8093 (t70) REVERT: Z 371 LEU cc_start: 0.8824 (mp) cc_final: 0.8492 (mp) REVERT: Z 422 MET cc_start: 0.8571 (mtp) cc_final: 0.8178 (mmm) REVERT: Z 504 LYS cc_start: 0.6789 (pttt) cc_final: 0.6029 (ptpt) REVERT: Z 546 GLU cc_start: 0.5315 (pm20) cc_final: 0.4505 (tm-30) REVERT: Z 550 LYS cc_start: 0.7049 (tppt) cc_final: 0.6191 (tptp) outliers start: 105 outliers final: 36 residues processed: 532 average time/residue: 0.6949 time to fit residues: 446.5763 Evaluate side-chains 428 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 382 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 475 GLU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 456 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 62 optimal weight: 5.9990 chunk 360 optimal weight: 0.3980 chunk 279 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 410 optimal weight: 0.0980 chunk 321 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 423 optimal weight: 0.0770 chunk 35 optimal weight: 8.9990 chunk 409 optimal weight: 0.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN P 52 GLN P 76 GLN S 195 ASN T 497 GLN U 60 GLN U 241 HIS ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 529 ASN ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 311 GLN Z 388 ASN Z 440 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.147889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109039 restraints weight = 49073.663| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.96 r_work: 0.3228 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34420 Z= 0.104 Angle : 0.522 9.515 46649 Z= 0.263 Chirality : 0.042 0.278 5520 Planarity : 0.004 0.050 5999 Dihedral : 6.609 158.458 4921 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.96 % Favored : 96.93 % Rotamer: Outliers : 2.66 % Allowed : 17.22 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.50 (0.13), residues: 4462 helix: 0.28 (0.11), residues: 2178 sheet: -0.83 (0.22), residues: 543 loop : -0.79 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 91 TYR 0.025 0.001 TYR U 453 PHE 0.021 0.001 PHE E 107 TRP 0.004 0.001 TRP P 58 HIS 0.003 0.001 HIS S 237 Details of bonding type rmsd covalent geometry : bond 0.00231 (34420) covalent geometry : angle 0.52212 (46649) hydrogen bonds : bond 0.03352 ( 1441) hydrogen bonds : angle 4.07378 ( 4182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 454 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6066 (mt) cc_final: 0.5697 (tp) REVERT: A 81 MET cc_start: 0.8518 (tmm) cc_final: 0.8088 (ppp) REVERT: A 92 ASN cc_start: 0.8508 (t0) cc_final: 0.8162 (t0) REVERT: A 95 ILE cc_start: 0.7363 (mp) cc_final: 0.7030 (tt) REVERT: B 107 PHE cc_start: 0.7490 (t80) cc_final: 0.6840 (t80) REVERT: C 102 TYR cc_start: 0.8322 (m-80) cc_final: 0.8096 (m-80) REVERT: E 71 LEU cc_start: 0.6620 (mm) cc_final: 0.6329 (mp) REVERT: E 91 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7800 (mtm180) REVERT: E 92 ASN cc_start: 0.8182 (t0) cc_final: 0.7919 (t0) REVERT: E 95 ILE cc_start: 0.8104 (pt) cc_final: 0.7739 (pt) REVERT: E 109 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7043 (tp) REVERT: E 119 LEU cc_start: 0.6436 (tp) cc_final: 0.6083 (mt) REVERT: F 109 LEU cc_start: 0.7054 (mt) cc_final: 0.6800 (mp) REVERT: H 126 PHE cc_start: 0.6204 (m-80) cc_final: 0.4732 (p90) REVERT: I 81 MET cc_start: 0.7551 (ttp) cc_final: 0.7308 (ttp) REVERT: I 119 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.5228 (mt) REVERT: P 150 LYS cc_start: 0.6831 (mmtp) cc_final: 0.6179 (mmmt) REVERT: Q 38 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7724 (mmtm) REVERT: Q 48 ARG cc_start: 0.8226 (ppt-90) cc_final: 0.7642 (ptt180) REVERT: R 110 GLN cc_start: 0.8975 (tt0) cc_final: 0.8637 (tt0) REVERT: R 171 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6141 (pp30) REVERT: S 147 ARG cc_start: 0.7561 (ptt90) cc_final: 0.6659 (ptm-80) REVERT: S 243 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8091 (mp) REVERT: S 248 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8230 (mt-10) REVERT: T 86 ARG cc_start: 0.8429 (mpp-170) cc_final: 0.8160 (mtt90) REVERT: T 456 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8339 (p) REVERT: U 149 GLN cc_start: 0.8163 (mt0) cc_final: 0.7932 (pt0) REVERT: U 199 ARG cc_start: 0.7495 (mtt90) cc_final: 0.7198 (mtt90) REVERT: U 204 THR cc_start: 0.8987 (p) cc_final: 0.8761 (t) REVERT: U 475 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: U 482 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: U 511 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6029 (mtmt) REVERT: U 537 LYS cc_start: 0.8137 (tptt) cc_final: 0.7821 (tptp) REVERT: U 549 HIS cc_start: 0.7424 (m90) cc_final: 0.7097 (m90) REVERT: U 551 LYS cc_start: 0.7513 (mttt) cc_final: 0.7154 (mtpt) REVERT: U 559 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6703 (mt) REVERT: V 467 ASP cc_start: 0.5920 (m-30) cc_final: 0.5279 (t0) REVERT: X 101 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8675 (ttpp) REVERT: X 158 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: X 326 THR cc_start: 0.8166 (p) cc_final: 0.7939 (p) REVERT: X 390 ASN cc_start: 0.8459 (m110) cc_final: 0.8138 (t0) REVERT: Y 215 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: Y 344 ASP cc_start: 0.8124 (t0) cc_final: 0.7703 (t0) REVERT: Y 430 LYS cc_start: 0.6656 (ttmt) cc_final: 0.6314 (mtmt) REVERT: Y 487 TYR cc_start: 0.7412 (t80) cc_final: 0.6603 (t80) REVERT: Y 488 MET cc_start: 0.7917 (mmm) cc_final: 0.6929 (mpt) REVERT: Y 501 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6583 (tmtp) REVERT: Z 51 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8339 (ttm110) REVERT: Z 82 ASP cc_start: 0.8351 (t0) cc_final: 0.8066 (t70) REVERT: Z 371 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8476 (mp) REVERT: Z 395 GLU cc_start: 0.8143 (tt0) cc_final: 0.7913 (pm20) REVERT: Z 422 MET cc_start: 0.8534 (mtp) cc_final: 0.8170 (mmm) REVERT: Z 437 ARG cc_start: 0.8669 (mtm180) cc_final: 0.8442 (mtm110) REVERT: Z 504 LYS cc_start: 0.6852 (pttt) cc_final: 0.6052 (ptpt) REVERT: Z 550 LYS cc_start: 0.7081 (tppt) cc_final: 0.6215 (tptp) outliers start: 95 outliers final: 34 residues processed: 519 average time/residue: 0.6858 time to fit residues: 430.3769 Evaluate side-chains 437 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 388 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 475 GLU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 558 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 426 SER Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 128 optimal weight: 0.6980 chunk 390 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 433 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 81 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 183 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN P 52 GLN P 83 GLN R 53 ASN S 276 ASN T 497 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 GLN U 386 GLN U 471 GLN U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109940 restraints weight = 49510.256| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.99 r_work: 0.3227 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34420 Z= 0.102 Angle : 0.521 9.531 46649 Z= 0.261 Chirality : 0.042 0.228 5520 Planarity : 0.003 0.049 5999 Dihedral : 6.397 171.932 4921 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.96 % Favored : 96.93 % Rotamer: Outliers : 2.95 % Allowed : 18.09 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.13), residues: 4462 helix: 0.51 (0.11), residues: 2196 sheet: -0.67 (0.22), residues: 546 loop : -0.59 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 91 TYR 0.023 0.001 TYR U 453 PHE 0.015 0.001 PHE F 107 TRP 0.004 0.001 TRP P 58 HIS 0.003 0.001 HIS S 237 Details of bonding type rmsd covalent geometry : bond 0.00226 (34420) covalent geometry : angle 0.52137 (46649) hydrogen bonds : bond 0.03296 ( 1441) hydrogen bonds : angle 3.97935 ( 4182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 448 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6144 (mt) cc_final: 0.5685 (tp) REVERT: A 81 MET cc_start: 0.8546 (tmm) cc_final: 0.8175 (ppp) REVERT: A 92 ASN cc_start: 0.8477 (t0) cc_final: 0.8123 (t0) REVERT: A 95 ILE cc_start: 0.7403 (mp) cc_final: 0.7110 (tt) REVERT: B 68 THR cc_start: 0.6638 (OUTLIER) cc_final: 0.6335 (p) REVERT: B 78 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7045 (mp) REVERT: E 71 LEU cc_start: 0.6556 (mm) cc_final: 0.6238 (mp) REVERT: E 91 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7834 (mmm160) REVERT: E 92 ASN cc_start: 0.8170 (t0) cc_final: 0.7887 (t0) REVERT: E 95 ILE cc_start: 0.8143 (pt) cc_final: 0.7794 (pt) REVERT: E 119 LEU cc_start: 0.6468 (tp) cc_final: 0.6093 (mt) REVERT: I 115 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.5669 (pp) REVERT: P 79 GLU cc_start: 0.8059 (tt0) cc_final: 0.7249 (tp30) REVERT: P 83 GLN cc_start: 0.8097 (mt0) cc_final: 0.7708 (mt0) REVERT: Q 38 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7690 (mmtm) REVERT: Q 48 ARG cc_start: 0.8241 (ppt-90) cc_final: 0.7961 (ptt180) REVERT: R 110 GLN cc_start: 0.8984 (tt0) cc_final: 0.8693 (tt0) REVERT: R 171 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.6118 (pp30) REVERT: S 75 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8599 (t) REVERT: S 147 ARG cc_start: 0.7516 (ptt90) cc_final: 0.6594 (ptm-80) REVERT: S 243 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8144 (mp) REVERT: S 248 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8230 (mt-10) REVERT: S 284 MET cc_start: 0.8630 (ttm) cc_final: 0.8427 (ptp) REVERT: T 86 ARG cc_start: 0.8422 (mpp-170) cc_final: 0.8148 (mtt90) REVERT: T 456 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8316 (p) REVERT: T 482 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7958 (mp0) REVERT: U 57 TYR cc_start: 0.7026 (p90) cc_final: 0.6584 (p90) REVERT: U 60 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6887 (mp-120) REVERT: U 199 ARG cc_start: 0.7533 (mtt90) cc_final: 0.7142 (mtt90) REVERT: U 204 THR cc_start: 0.9006 (p) cc_final: 0.8792 (t) REVERT: U 475 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: U 482 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: U 511 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.5963 (mtmt) REVERT: U 537 LYS cc_start: 0.8166 (tptt) cc_final: 0.7864 (tptp) REVERT: U 551 LYS cc_start: 0.7657 (mttt) cc_final: 0.7202 (mtpt) REVERT: U 559 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6665 (mt) REVERT: V 467 ASP cc_start: 0.5811 (m-30) cc_final: 0.5196 (t0) REVERT: X 158 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: X 326 THR cc_start: 0.8153 (p) cc_final: 0.7952 (p) REVERT: X 390 ASN cc_start: 0.8440 (m110) cc_final: 0.8129 (t0) REVERT: Y 215 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: Y 344 ASP cc_start: 0.8105 (t0) cc_final: 0.7674 (t0) REVERT: Y 430 LYS cc_start: 0.6641 (ttmt) cc_final: 0.6345 (mtmt) REVERT: Y 487 TYR cc_start: 0.7361 (t80) cc_final: 0.6880 (t80) REVERT: Y 488 MET cc_start: 0.7946 (mmm) cc_final: 0.6946 (mpt) REVERT: Y 501 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6584 (ttpt) REVERT: Z 51 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8283 (ttm110) REVERT: Z 82 ASP cc_start: 0.8334 (t0) cc_final: 0.8100 (t70) REVERT: Z 371 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8455 (mp) REVERT: Z 422 MET cc_start: 0.8543 (mtp) cc_final: 0.8167 (mmm) REVERT: Z 437 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8426 (mtm110) REVERT: Z 504 LYS cc_start: 0.6806 (pttt) cc_final: 0.6087 (ptpt) REVERT: Z 527 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7358 (tp) REVERT: Z 550 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6073 (tptp) REVERT: Z 572 LYS cc_start: 0.8552 (tppt) cc_final: 0.7553 (mmtm) outliers start: 105 outliers final: 40 residues processed: 515 average time/residue: 0.6999 time to fit residues: 433.8241 Evaluate side-chains 452 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 393 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 83 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 475 GLU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 558 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 325 ILE Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 183 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 397 optimal weight: 0.0870 chunk 125 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 231 optimal weight: 0.0670 chunk 308 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 438 optimal weight: 9.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN J 92 ASN P 52 GLN R 139 ASN T 497 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.148248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110754 restraints weight = 49312.560| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.00 r_work: 0.3239 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34420 Z= 0.105 Angle : 0.526 9.699 46649 Z= 0.262 Chirality : 0.042 0.250 5520 Planarity : 0.003 0.049 5999 Dihedral : 6.234 169.329 4921 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.86 % Rotamer: Outliers : 3.06 % Allowed : 18.54 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.05 (0.13), residues: 4462 helix: 0.70 (0.12), residues: 2188 sheet: -0.60 (0.22), residues: 552 loop : -0.47 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 91 TYR 0.023 0.001 TYR U 453 PHE 0.023 0.001 PHE E 107 TRP 0.004 0.001 TRP P 58 HIS 0.007 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00233 (34420) covalent geometry : angle 0.52567 (46649) hydrogen bonds : bond 0.03256 ( 1441) hydrogen bonds : angle 3.95480 ( 4182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 426 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6098 (mt) cc_final: 0.5815 (tp) REVERT: A 92 ASN cc_start: 0.8469 (t0) cc_final: 0.8105 (t0) REVERT: A 95 ILE cc_start: 0.7414 (mp) cc_final: 0.7042 (tt) REVERT: B 68 THR cc_start: 0.6640 (OUTLIER) cc_final: 0.6320 (p) REVERT: B 107 PHE cc_start: 0.7644 (t80) cc_final: 0.7360 (t80) REVERT: E 71 LEU cc_start: 0.6536 (mm) cc_final: 0.6183 (mp) REVERT: E 91 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7833 (mmm160) REVERT: E 92 ASN cc_start: 0.8137 (t0) cc_final: 0.7909 (t0) REVERT: E 95 ILE cc_start: 0.8151 (pt) cc_final: 0.7805 (pt) REVERT: E 119 LEU cc_start: 0.6598 (tp) cc_final: 0.6234 (mt) REVERT: Q 38 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7629 (mmtm) REVERT: Q 48 ARG cc_start: 0.8226 (ppt-90) cc_final: 0.7910 (ptt180) REVERT: R 58 LYS cc_start: 0.7691 (mmtp) cc_final: 0.7438 (tptt) REVERT: R 110 GLN cc_start: 0.8980 (tt0) cc_final: 0.8646 (tt0) REVERT: R 171 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6123 (pp30) REVERT: S 147 ARG cc_start: 0.7412 (ptt90) cc_final: 0.6565 (ptm-80) REVERT: S 243 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8165 (mp) REVERT: S 248 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8187 (mt-10) REVERT: T 86 ARG cc_start: 0.8423 (mpp-170) cc_final: 0.8145 (mtt90) REVERT: T 448 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8057 (tp) REVERT: T 456 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8302 (p) REVERT: T 482 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7843 (mp0) REVERT: U 57 TYR cc_start: 0.6932 (p90) cc_final: 0.6507 (p90) REVERT: U 199 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7147 (mtt90) REVERT: U 476 ARG cc_start: 0.7037 (tpt-90) cc_final: 0.6658 (ttt-90) REVERT: U 487 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8124 (mtpt) REVERT: U 511 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.5979 (mtmt) REVERT: U 537 LYS cc_start: 0.8160 (tptt) cc_final: 0.7837 (tptp) REVERT: U 551 LYS cc_start: 0.7602 (mttt) cc_final: 0.7201 (mtpt) REVERT: U 559 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6608 (mt) REVERT: X 158 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: X 390 ASN cc_start: 0.8412 (m110) cc_final: 0.8129 (t0) REVERT: X 484 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: Y 344 ASP cc_start: 0.8098 (t0) cc_final: 0.7672 (t0) REVERT: Y 430 LYS cc_start: 0.6729 (ttmt) cc_final: 0.6432 (mtmt) REVERT: Y 501 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6618 (ttpt) REVERT: Z 51 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8242 (ttm110) REVERT: Z 82 ASP cc_start: 0.8239 (t0) cc_final: 0.8001 (t70) REVERT: Z 371 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8445 (mp) REVERT: Z 422 MET cc_start: 0.8556 (mtp) cc_final: 0.8188 (mmm) REVERT: Z 527 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7392 (tp) REVERT: Z 546 GLU cc_start: 0.5352 (pp20) cc_final: 0.4660 (tm-30) REVERT: Z 550 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6203 (tptp) REVERT: Z 572 LYS cc_start: 0.8565 (tppt) cc_final: 0.7570 (mmtm) outliers start: 109 outliers final: 43 residues processed: 509 average time/residue: 0.7037 time to fit residues: 433.0909 Evaluate side-chains 454 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 396 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain U residue 83 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 404 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 429 optimal weight: 0.6980 chunk 340 optimal weight: 0.9980 chunk 352 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 441 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN P 52 GLN P 83 GLN R 53 ASN T 497 GLN ** U 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 414 GLN Z 440 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109881 restraints weight = 49393.753| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.96 r_work: 0.3223 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34420 Z= 0.122 Angle : 0.548 10.473 46649 Z= 0.272 Chirality : 0.043 0.272 5520 Planarity : 0.004 0.050 5999 Dihedral : 6.137 146.579 4921 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 2.72 % Allowed : 19.38 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.09 (0.13), residues: 4462 helix: 0.71 (0.12), residues: 2191 sheet: -0.55 (0.22), residues: 552 loop : -0.42 (0.16), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 476 TYR 0.022 0.001 TYR U 453 PHE 0.023 0.001 PHE B 107 TRP 0.004 0.001 TRP U 73 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00281 (34420) covalent geometry : angle 0.54847 (46649) hydrogen bonds : bond 0.03389 ( 1441) hydrogen bonds : angle 3.98622 ( 4182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 420 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6061 (mt) cc_final: 0.5701 (tp) REVERT: A 81 MET cc_start: 0.8576 (tmm) cc_final: 0.8102 (ppp) REVERT: A 92 ASN cc_start: 0.8493 (t0) cc_final: 0.8110 (t0) REVERT: A 95 ILE cc_start: 0.7454 (mp) cc_final: 0.7196 (tt) REVERT: B 68 THR cc_start: 0.6526 (OUTLIER) cc_final: 0.6195 (p) REVERT: B 115 LEU cc_start: 0.5613 (mm) cc_final: 0.5280 (pt) REVERT: D 61 MET cc_start: 0.5297 (mtp) cc_final: 0.4938 (ptp) REVERT: E 71 LEU cc_start: 0.6676 (mm) cc_final: 0.6241 (mp) REVERT: E 91 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7815 (mmm160) REVERT: E 92 ASN cc_start: 0.8140 (t0) cc_final: 0.7880 (t0) REVERT: E 95 ILE cc_start: 0.8165 (pt) cc_final: 0.7815 (pt) REVERT: E 119 LEU cc_start: 0.6641 (tp) cc_final: 0.6251 (mt) REVERT: J 81 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7620 (mtp) REVERT: P 79 GLU cc_start: 0.7877 (tt0) cc_final: 0.7073 (tp30) REVERT: Q 38 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7696 (mmtm) REVERT: Q 48 ARG cc_start: 0.8194 (ppt-90) cc_final: 0.7879 (ptt180) REVERT: R 31 LYS cc_start: 0.7608 (pmtt) cc_final: 0.6998 (ttpp) REVERT: R 58 LYS cc_start: 0.7677 (mmtp) cc_final: 0.7408 (tptt) REVERT: R 110 GLN cc_start: 0.8976 (tt0) cc_final: 0.8663 (tt0) REVERT: R 171 GLN cc_start: 0.6658 (OUTLIER) cc_final: 0.6123 (pp30) REVERT: S 147 ARG cc_start: 0.7399 (ptt90) cc_final: 0.6574 (ptm-80) REVERT: S 243 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8143 (mp) REVERT: T 448 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8111 (tp) REVERT: T 483 MET cc_start: 0.7412 (tpt) cc_final: 0.6960 (tpt) REVERT: T 522 GLU cc_start: 0.7054 (pp20) cc_final: 0.6573 (pp20) REVERT: U 57 TYR cc_start: 0.7087 (p90) cc_final: 0.6690 (p90) REVERT: U 199 ARG cc_start: 0.7546 (mtt90) cc_final: 0.7279 (mtt90) REVERT: U 487 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7709 (mtmm) REVERT: U 511 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6061 (mtmt) REVERT: U 537 LYS cc_start: 0.8208 (tptt) cc_final: 0.7918 (tptp) REVERT: U 551 LYS cc_start: 0.7575 (mttt) cc_final: 0.7222 (mtpt) REVERT: U 559 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6674 (mt) REVERT: X 101 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8203 (mmtm) REVERT: X 158 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: X 484 MET cc_start: 0.6682 (tmt) cc_final: 0.6420 (tmm) REVERT: Y 344 ASP cc_start: 0.8077 (t0) cc_final: 0.7650 (t0) REVERT: Y 430 LYS cc_start: 0.6816 (ttmt) cc_final: 0.6483 (mtmt) REVERT: Y 501 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6639 (ttpt) REVERT: Z 51 ARG cc_start: 0.8507 (ttm-80) cc_final: 0.8259 (ttm110) REVERT: Z 82 ASP cc_start: 0.8366 (t0) cc_final: 0.8073 (t70) REVERT: Z 371 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8480 (mp) REVERT: Z 422 MET cc_start: 0.8486 (mtp) cc_final: 0.8124 (mmm) REVERT: Z 527 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7432 (tp) REVERT: Z 550 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6284 (tptp) REVERT: Z 572 LYS cc_start: 0.8595 (tppt) cc_final: 0.7590 (mmtm) outliers start: 97 outliers final: 49 residues processed: 487 average time/residue: 0.7042 time to fit residues: 413.8761 Evaluate side-chains 446 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 382 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 188 LYS Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain U residue 83 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 558 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 419 ILE Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 86 optimal weight: 3.9990 chunk 167 optimal weight: 0.3980 chunk 29 optimal weight: 10.0000 chunk 339 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 366 optimal weight: 4.9990 chunk 390 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 267 optimal weight: 0.4980 chunk 302 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN I 92 ASN J 92 ASN P 52 GLN T 497 GLN ** U 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Y 337 GLN Y 414 GLN Z 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108827 restraints weight = 49225.620| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.00 r_work: 0.3221 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34420 Z= 0.120 Angle : 0.560 10.446 46649 Z= 0.277 Chirality : 0.043 0.319 5520 Planarity : 0.004 0.052 5999 Dihedral : 5.977 122.728 4921 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.52 % Allowed : 20.14 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.18 (0.13), residues: 4462 helix: 0.78 (0.12), residues: 2187 sheet: -0.52 (0.22), residues: 552 loop : -0.36 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 441 TYR 0.016 0.001 TYR Z 248 PHE 0.020 0.001 PHE E 116 TRP 0.003 0.001 TRP P 58 HIS 0.005 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00274 (34420) covalent geometry : angle 0.56024 (46649) hydrogen bonds : bond 0.03357 ( 1441) hydrogen bonds : angle 3.97349 ( 4182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 395 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6231 (mt) cc_final: 0.5752 (tp) REVERT: A 81 MET cc_start: 0.8544 (tmm) cc_final: 0.8297 (ppp) REVERT: A 92 ASN cc_start: 0.8550 (t0) cc_final: 0.8147 (t0) REVERT: A 95 ILE cc_start: 0.7444 (mp) cc_final: 0.7146 (tt) REVERT: A 122 PHE cc_start: 0.4998 (OUTLIER) cc_final: 0.4533 (p90) REVERT: B 68 THR cc_start: 0.6520 (OUTLIER) cc_final: 0.6181 (p) REVERT: B 81 MET cc_start: 0.7828 (ptm) cc_final: 0.7451 (ptp) REVERT: C 61 MET cc_start: 0.4727 (OUTLIER) cc_final: 0.4453 (mmp) REVERT: D 81 MET cc_start: 0.8132 (tmm) cc_final: 0.7930 (tmm) REVERT: D 113 ILE cc_start: 0.7138 (mp) cc_final: 0.6888 (mp) REVERT: E 71 LEU cc_start: 0.6730 (mm) cc_final: 0.6300 (mp) REVERT: E 91 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7823 (mmm160) REVERT: E 92 ASN cc_start: 0.8124 (t0) cc_final: 0.7871 (t0) REVERT: E 95 ILE cc_start: 0.8153 (pt) cc_final: 0.7789 (pt) REVERT: E 119 LEU cc_start: 0.6550 (tp) cc_final: 0.6188 (mt) REVERT: G 113 ILE cc_start: 0.4704 (OUTLIER) cc_final: 0.4400 (pp) REVERT: J 81 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7782 (mtp) REVERT: P 79 GLU cc_start: 0.7863 (tt0) cc_final: 0.7103 (tp30) REVERT: P 83 GLN cc_start: 0.8113 (mt0) cc_final: 0.7778 (mt0) REVERT: P 150 LYS cc_start: 0.7193 (mmtp) cc_final: 0.6592 (mmmt) REVERT: Q 48 ARG cc_start: 0.8190 (ppt-90) cc_final: 0.7859 (ptt180) REVERT: R 31 LYS cc_start: 0.7648 (pmtt) cc_final: 0.7043 (ttpp) REVERT: R 58 LYS cc_start: 0.7643 (mmtp) cc_final: 0.7360 (tptt) REVERT: R 110 GLN cc_start: 0.8987 (tt0) cc_final: 0.8680 (tt0) REVERT: R 171 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6119 (pp30) REVERT: S 147 ARG cc_start: 0.7454 (ptt90) cc_final: 0.6577 (ptm-80) REVERT: S 243 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8167 (mp) REVERT: T 522 GLU cc_start: 0.7127 (pp20) cc_final: 0.6641 (pp20) REVERT: U 92 ASP cc_start: 0.8408 (m-30) cc_final: 0.8200 (m-30) REVERT: U 199 ARG cc_start: 0.7501 (mtt90) cc_final: 0.7218 (mtt90) REVERT: U 453 TYR cc_start: 0.7263 (t80) cc_final: 0.6486 (t80) REVERT: U 476 ARG cc_start: 0.7052 (tpt-90) cc_final: 0.6817 (tpt-90) REVERT: U 487 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8060 (mtpt) REVERT: U 511 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6068 (mtmt) REVERT: U 537 LYS cc_start: 0.8284 (tptt) cc_final: 0.7986 (tptp) REVERT: U 551 LYS cc_start: 0.7554 (mttt) cc_final: 0.7245 (mtpt) REVERT: U 559 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6674 (mt) REVERT: X 158 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: X 484 MET cc_start: 0.6706 (tmt) cc_final: 0.6448 (tmm) REVERT: X 491 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6690 (p0) REVERT: Y 344 ASP cc_start: 0.8098 (t0) cc_final: 0.7661 (t0) REVERT: Y 430 LYS cc_start: 0.6811 (ttmt) cc_final: 0.6480 (mtmt) REVERT: Y 501 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6623 (ttpt) REVERT: Z 51 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8268 (ttm110) REVERT: Z 82 ASP cc_start: 0.8373 (t0) cc_final: 0.8093 (t70) REVERT: Z 371 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8466 (mp) REVERT: Z 422 MET cc_start: 0.8488 (mtp) cc_final: 0.8132 (mmm) REVERT: Z 527 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7426 (tp) REVERT: Z 546 GLU cc_start: 0.5375 (pp20) cc_final: 0.4754 (tm-30) REVERT: Z 550 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6251 (tptp) REVERT: Z 572 LYS cc_start: 0.8609 (tppt) cc_final: 0.7595 (mmtm) outliers start: 90 outliers final: 47 residues processed: 461 average time/residue: 0.7050 time to fit residues: 391.3985 Evaluate side-chains 436 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 373 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain U residue 83 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 419 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 527 LEU Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 115 optimal weight: 6.9990 chunk 351 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 chunk 438 optimal weight: 0.9980 chunk 241 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 408 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN Q 46 HIS T 497 GLN ** U 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Y 322 GLN Y 337 GLN Z 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.147614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109183 restraints weight = 49271.796| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.78 r_work: 0.3230 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34420 Z= 0.115 Angle : 0.564 12.344 46649 Z= 0.278 Chirality : 0.043 0.297 5520 Planarity : 0.004 0.065 5999 Dihedral : 5.824 104.372 4921 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 2.22 % Allowed : 20.59 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.26 (0.13), residues: 4462 helix: 0.84 (0.12), residues: 2186 sheet: -0.44 (0.22), residues: 549 loop : -0.34 (0.16), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 199 TYR 0.022 0.001 TYR P 75 PHE 0.028 0.001 PHE E 116 TRP 0.003 0.001 TRP P 58 HIS 0.004 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00263 (34420) covalent geometry : angle 0.56397 (46649) hydrogen bonds : bond 0.03308 ( 1441) hydrogen bonds : angle 3.96277 ( 4182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 408 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6235 (mt) cc_final: 0.5857 (tp) REVERT: A 81 MET cc_start: 0.8562 (tmm) cc_final: 0.8150 (ppp) REVERT: A 91 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7014 (mtt-85) REVERT: A 92 ASN cc_start: 0.8463 (t0) cc_final: 0.8069 (t0) REVERT: A 95 ILE cc_start: 0.7518 (mp) cc_final: 0.7226 (tt) REVERT: A 122 PHE cc_start: 0.4965 (OUTLIER) cc_final: 0.4452 (p90) REVERT: B 68 THR cc_start: 0.6510 (OUTLIER) cc_final: 0.6189 (p) REVERT: B 81 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7454 (ptp) REVERT: B 115 LEU cc_start: 0.5668 (mm) cc_final: 0.5275 (pt) REVERT: C 61 MET cc_start: 0.4736 (OUTLIER) cc_final: 0.4463 (mmp) REVERT: C 118 LEU cc_start: 0.7077 (tp) cc_final: 0.6814 (tm) REVERT: D 61 MET cc_start: 0.5168 (mtp) cc_final: 0.4878 (ptp) REVERT: D 113 ILE cc_start: 0.7157 (mp) cc_final: 0.6910 (mp) REVERT: E 71 LEU cc_start: 0.6743 (mm) cc_final: 0.6309 (mp) REVERT: E 91 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7788 (mmm160) REVERT: E 92 ASN cc_start: 0.8073 (t0) cc_final: 0.7802 (t0) REVERT: E 95 ILE cc_start: 0.8142 (pt) cc_final: 0.7776 (pt) REVERT: E 119 LEU cc_start: 0.6524 (tp) cc_final: 0.6139 (mt) REVERT: F 118 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7259 (mt) REVERT: G 113 ILE cc_start: 0.4718 (OUTLIER) cc_final: 0.4483 (pp) REVERT: I 81 MET cc_start: 0.7109 (ttt) cc_final: 0.6770 (ttp) REVERT: P 79 GLU cc_start: 0.7794 (tt0) cc_final: 0.7062 (tp30) REVERT: P 83 GLN cc_start: 0.8114 (mt0) cc_final: 0.7798 (mt0) REVERT: P 150 LYS cc_start: 0.7210 (mmtp) cc_final: 0.6047 (tmmt) REVERT: Q 48 ARG cc_start: 0.8147 (ppt-90) cc_final: 0.7815 (ptt180) REVERT: R 31 LYS cc_start: 0.7650 (pmtt) cc_final: 0.7084 (ttpp) REVERT: R 58 LYS cc_start: 0.7647 (mmtp) cc_final: 0.7359 (tptt) REVERT: R 110 GLN cc_start: 0.8958 (tt0) cc_final: 0.8687 (tt0) REVERT: R 171 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.6113 (pp30) REVERT: S 147 ARG cc_start: 0.7395 (ptt90) cc_final: 0.6559 (ptm-80) REVERT: S 243 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8131 (mp) REVERT: U 199 ARG cc_start: 0.7479 (mtt90) cc_final: 0.7193 (mtt90) REVERT: U 453 TYR cc_start: 0.7315 (t80) cc_final: 0.6477 (t80) REVERT: U 487 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8020 (mtpt) REVERT: U 511 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6047 (mtmt) REVERT: U 537 LYS cc_start: 0.8268 (tptt) cc_final: 0.7960 (tptp) REVERT: U 551 LYS cc_start: 0.7492 (mttt) cc_final: 0.7065 (mtpt) REVERT: U 559 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6574 (mt) REVERT: X 101 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8144 (mmtm) REVERT: X 158 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: X 484 MET cc_start: 0.6691 (tmt) cc_final: 0.6447 (tmm) REVERT: X 491 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6677 (p0) REVERT: X 501 LYS cc_start: 0.7268 (ttmm) cc_final: 0.7017 (tppt) REVERT: Y 292 GLN cc_start: 0.8480 (tt0) cc_final: 0.8012 (tt0) REVERT: Y 344 ASP cc_start: 0.8078 (t0) cc_final: 0.7643 (t0) REVERT: Y 430 LYS cc_start: 0.6800 (ttmt) cc_final: 0.6465 (mtmt) REVERT: Y 501 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6603 (ttpt) REVERT: Z 51 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8246 (ttm110) REVERT: Z 82 ASP cc_start: 0.8367 (t0) cc_final: 0.8088 (t70) REVERT: Z 371 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8447 (mp) REVERT: Z 422 MET cc_start: 0.8483 (mtp) cc_final: 0.8096 (mmm) REVERT: Z 550 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6268 (tptp) REVERT: Z 572 LYS cc_start: 0.8596 (tppt) cc_final: 0.7597 (mmtm) outliers start: 79 outliers final: 46 residues processed: 469 average time/residue: 0.7279 time to fit residues: 410.9885 Evaluate side-chains 452 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 389 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain U residue 83 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 158 GLU Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 267 optimal weight: 0.0000 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 404 optimal weight: 0.9990 chunk 412 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 380 optimal weight: 7.9990 chunk 305 optimal weight: 0.6980 chunk 287 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN T 497 GLN ** U 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 441 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Y 337 GLN Y 414 GLN Z 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.147606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108805 restraints weight = 49443.046| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.99 r_work: 0.3221 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34420 Z= 0.119 Angle : 0.570 12.077 46649 Z= 0.282 Chirality : 0.043 0.383 5520 Planarity : 0.004 0.077 5999 Dihedral : 5.752 90.988 4921 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 2.27 % Allowed : 20.53 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.29 (0.13), residues: 4462 helix: 0.86 (0.12), residues: 2188 sheet: -0.45 (0.22), residues: 549 loop : -0.31 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 476 TYR 0.017 0.001 TYR Z 248 PHE 0.036 0.001 PHE E 116 TRP 0.003 0.001 TRP P 58 HIS 0.004 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00273 (34420) covalent geometry : angle 0.57020 (46649) hydrogen bonds : bond 0.03349 ( 1441) hydrogen bonds : angle 3.97347 ( 4182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 403 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6186 (mt) cc_final: 0.5781 (tp) REVERT: A 81 MET cc_start: 0.8550 (tmm) cc_final: 0.8209 (ppp) REVERT: A 91 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7040 (mtt-85) REVERT: A 92 ASN cc_start: 0.8506 (t0) cc_final: 0.8102 (t0) REVERT: A 95 ILE cc_start: 0.7588 (mp) cc_final: 0.7317 (tt) REVERT: A 122 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.4506 (p90) REVERT: B 68 THR cc_start: 0.6529 (OUTLIER) cc_final: 0.6206 (p) REVERT: B 81 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7554 (ptp) REVERT: C 118 LEU cc_start: 0.7027 (tp) cc_final: 0.6765 (tm) REVERT: D 61 MET cc_start: 0.5140 (mtp) cc_final: 0.4836 (ptp) REVERT: D 113 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6841 (mp) REVERT: E 71 LEU cc_start: 0.6715 (mm) cc_final: 0.6295 (mp) REVERT: E 91 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7840 (mmm160) REVERT: E 92 ASN cc_start: 0.8103 (t0) cc_final: 0.7861 (t0) REVERT: E 95 ILE cc_start: 0.8170 (pt) cc_final: 0.7808 (pt) REVERT: E 119 LEU cc_start: 0.6275 (tp) cc_final: 0.5910 (mt) REVERT: I 81 MET cc_start: 0.7088 (ttt) cc_final: 0.6746 (ttp) REVERT: J 61 MET cc_start: 0.4403 (mtt) cc_final: 0.4123 (tpp) REVERT: P 79 GLU cc_start: 0.7815 (tt0) cc_final: 0.7060 (tp30) REVERT: P 83 GLN cc_start: 0.8114 (mt0) cc_final: 0.7717 (mt0) REVERT: P 150 LYS cc_start: 0.7286 (mmtp) cc_final: 0.6125 (tmmt) REVERT: Q 48 ARG cc_start: 0.8186 (ppt-90) cc_final: 0.7851 (ptt180) REVERT: Q 52 TYR cc_start: 0.7273 (m-10) cc_final: 0.7071 (m-10) REVERT: R 31 LYS cc_start: 0.7657 (pmtt) cc_final: 0.7064 (ttpp) REVERT: R 58 LYS cc_start: 0.7657 (mmtp) cc_final: 0.7373 (tptt) REVERT: R 110 GLN cc_start: 0.8972 (tt0) cc_final: 0.8675 (tt0) REVERT: R 171 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5942 (pp30) REVERT: S 147 ARG cc_start: 0.7415 (ptt90) cc_final: 0.6574 (ptm-80) REVERT: S 243 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8175 (mp) REVERT: T 456 VAL cc_start: 0.8552 (t) cc_final: 0.8257 (p) REVERT: U 57 TYR cc_start: 0.7231 (p90) cc_final: 0.6750 (p90) REVERT: U 199 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7194 (mtt90) REVERT: U 453 TYR cc_start: 0.7337 (t80) cc_final: 0.6509 (t80) REVERT: U 475 GLU cc_start: 0.7139 (tt0) cc_final: 0.6691 (pp20) REVERT: U 487 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7702 (mtmm) REVERT: U 511 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6098 (mtmt) REVERT: U 537 LYS cc_start: 0.8291 (tptt) cc_final: 0.7988 (tptp) REVERT: U 551 LYS cc_start: 0.7481 (mttt) cc_final: 0.7132 (mtpt) REVERT: U 559 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6663 (pp) REVERT: X 101 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8189 (mmtm) REVERT: X 158 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: X 491 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6719 (p0) REVERT: X 501 LYS cc_start: 0.7202 (ttmm) cc_final: 0.6926 (tppt) REVERT: Y 292 GLN cc_start: 0.8523 (tt0) cc_final: 0.8071 (tt0) REVERT: Y 344 ASP cc_start: 0.8117 (t0) cc_final: 0.7680 (t0) REVERT: Y 430 LYS cc_start: 0.6814 (ttmt) cc_final: 0.6477 (mtmt) REVERT: Y 488 MET cc_start: 0.7998 (mtp) cc_final: 0.7756 (tpp) REVERT: Y 501 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6648 (ttpt) REVERT: Z 51 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8272 (ttm110) REVERT: Z 82 ASP cc_start: 0.8381 (t0) cc_final: 0.8100 (t70) REVERT: Z 371 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8477 (mp) REVERT: Z 386 MET cc_start: 0.8867 (mmm) cc_final: 0.8650 (mmm) REVERT: Z 422 MET cc_start: 0.8458 (mtp) cc_final: 0.8072 (mmm) REVERT: Z 550 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6277 (tptp) REVERT: Z 558 THR cc_start: 0.8762 (t) cc_final: 0.8552 (t) REVERT: Z 572 LYS cc_start: 0.8608 (tppt) cc_final: 0.7609 (mmtm) outliers start: 81 outliers final: 46 residues processed: 463 average time/residue: 0.7172 time to fit residues: 401.6993 Evaluate side-chains 455 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 394 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 73 ILE Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain U residue 83 HIS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 267 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 511 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 113 SER Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 491 ASP Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain Y residue 82 ASP Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 161 VAL Chi-restraints excluded: chain Z residue 371 LEU Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 431 LEU Chi-restraints excluded: chain Z residue 456 THR Chi-restraints excluded: chain Z residue 550 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 368 optimal weight: 0.6980 chunk 270 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 165 optimal weight: 0.0170 chunk 242 optimal weight: 0.6980 chunk 15 optimal weight: 20.0000 chunk 265 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 325 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 418 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN H 87 ASN ** T 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN ** U 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 HIS ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Y 337 GLN Z 440 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.147586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109798 restraints weight = 49197.784| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.98 r_work: 0.3228 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.366 34420 Z= 0.186 Angle : 0.671 65.889 46649 Z= 0.362 Chirality : 0.043 0.382 5520 Planarity : 0.005 0.282 5999 Dihedral : 5.749 90.964 4921 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 1.96 % Allowed : 21.15 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.29 (0.13), residues: 4462 helix: 0.86 (0.12), residues: 2188 sheet: -0.45 (0.22), residues: 549 loop : -0.31 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 199 TYR 0.017 0.001 TYR D 102 PHE 0.027 0.001 PHE E 116 TRP 0.003 0.001 TRP P 58 HIS 0.004 0.001 HIS U 61 Details of bonding type rmsd covalent geometry : bond 0.00412 (34420) covalent geometry : angle 0.67110 (46649) hydrogen bonds : bond 0.03354 ( 1441) hydrogen bonds : angle 3.98161 ( 4182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14897.56 seconds wall clock time: 253 minutes 43.66 seconds (15223.66 seconds total)