Starting phenix.real_space_refine on Mon Sep 14 01:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c79_30296/09_2026/7c79_30296.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 331 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 16022 2.51 5 N 4808 2.21 5 O 6053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27324 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 7008 Classifications: {'RNAv2': 331} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 24, 'rna3p_pur': 140, 'rna3p_pyr': 147} Link IDs: {'rna2p': 44, 'rna3p': 286} Chain breaks: 1 Chain: "B" Number of atoms: 6453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6453 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 37, 'TRANS': 755} Chain breaks: 3 Chain: "C" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1246 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 11, 'TRANS': 140} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2086 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1135 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1271 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2253 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "K" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 840 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1110 Classifications: {'peptide': 131} Link IDs: {'TRANS': 130} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25908 SG CYS K 64 54.461 52.784 52.287 1.00118.09 S Time building chain proxies: 5.08, per 1000 atoms: 0.19 Number of scatterers: 27324 At special positions: 0 Unit cell: (141.9, 133.1, 210.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 331 15.00 Mg 1 11.99 O 6053 8.00 N 4808 7.00 C 16022 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: 2.66 Conformation dependent library (CDL) restraints added in 863.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 200 " pdb="ZN ZN K 200 " - pdb=" SG CYS K 64 " 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 17 sheets defined 45.1% alpha, 16.4% beta 41 base pairs and 135 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.896A pdb=" N ARG B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 78 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 143 through 163 removed outlier: 3.637A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.642A pdb=" N LYS B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 removed outlier: 3.814A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.606A pdb=" N HIS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.686A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.519A pdb=" N ARG B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.261A pdb=" N GLN B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.761A pdb=" N SER B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.928A pdb=" N MET B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 471 through 479 removed outlier: 4.220A pdb=" N ILE B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 564 through 574 removed outlier: 3.742A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 removed outlier: 3.712A pdb=" N ASN B 593 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 removed outlier: 3.505A pdb=" N TYR B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 removed outlier: 4.065A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 3.602A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 789 through 798 removed outlier: 3.500A pdb=" N LEU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 850 Processing helix chain 'C' and resid 40 through 56 removed outlier: 3.990A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 3.579A pdb=" N LEU C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.341A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.916A pdb=" N LYS D 15 " --> pdb=" O CYS D 11 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 26 removed outlier: 3.743A pdb=" N ASN D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 110 removed outlier: 3.697A pdb=" N ILE D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.605A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.608A pdb=" N TYR D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER D 132 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 126 through 133' Processing helix chain 'D' and resid 135 through 155 Proline residue: D 141 - end of helix removed outlier: 3.849A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 273 through 279 removed outlier: 4.012A pdb=" N ILE D 277 " --> pdb=" O MET D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.919A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 122 through 146 removed outlier: 3.738A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 4.077A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.791A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 removed outlier: 3.877A pdb=" N LYS F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.898A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 85 removed outlier: 3.694A pdb=" N ASP G 84 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 30 through 46 removed outlier: 3.782A pdb=" N TRP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.534A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.729A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 69 through 77 removed outlier: 3.610A pdb=" N ASP I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.978A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE I 104 " --> pdb=" O ILE I 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 104' Processing helix chain 'I' and resid 113 through 123 removed outlier: 3.575A pdb=" N LEU I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN I 123 " --> pdb=" O LEU I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 153 removed outlier: 3.592A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG I 152 " --> pdb=" O SER I 148 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I 153 " --> pdb=" O CYS I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.643A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 185 removed outlier: 4.236A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 3.578A pdb=" N SER I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 37 removed outlier: 3.636A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 4.306A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 3.834A pdb=" N ILE J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 Processing helix chain 'J' and resid 142 through 153 removed outlier: 4.074A pdb=" N ILE J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.781A pdb=" N LEU J 164 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 4.098A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.810A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 242 removed outlier: 3.502A pdb=" N LEU J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA J 229 " --> pdb=" O MET J 225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN J 240 " --> pdb=" O GLY J 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 removed outlier: 3.524A pdb=" N LYS K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 29 through 48 removed outlier: 3.686A pdb=" N TYR K 47 " --> pdb=" O SER K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 58 removed outlier: 4.538A pdb=" N GLY K 58 " --> pdb=" O GLN K 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 26 removed outlier: 3.521A pdb=" N LEU L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 58 removed outlier: 3.686A pdb=" N GLN L 58 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 79 removed outlier: 4.000A pdb=" N TRP L 67 " --> pdb=" O LYS L 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 68 " --> pdb=" O ASP L 64 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE L 79 " --> pdb=" O GLN L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 96 removed outlier: 4.415A pdb=" N ARG L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE L 93 " --> pdb=" O PHE L 89 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 131 removed outlier: 4.025A pdb=" N THR L 104 " --> pdb=" O THR L 100 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 115 " --> pdb=" O ASN L 111 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR L 125 " --> pdb=" O GLU L 121 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY L 131 " --> pdb=" O PHE L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.570A pdb=" N LEU B 57 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 33 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.061A pdb=" N GLY B 216 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 350 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN B 342 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 358 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE B 334 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 250 through 254 removed outlier: 6.546A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 450 removed outlier: 3.589A pdb=" N PHE B 448 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 762 through 769 removed outlier: 4.699A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN B 835 " --> pdb=" O TYR B 829 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR B 829 " --> pdb=" O ASN B 835 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET B 837 " --> pdb=" O GLY B 827 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY B 827 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 839 " --> pdb=" O THR B 825 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B 823 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE B 821 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.970A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.970A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AB1, first strand: chain 'E' and resid 73 through 78 removed outlier: 6.764A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.103A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 121 " --> pdb=" O GLY F 4 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 138 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 83 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.103A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 121 " --> pdb=" O GLY F 4 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'H' and resid 55 through 61 removed outlier: 8.815A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 103 " --> pdb=" O TYR H 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.523A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE I 45 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE I 87 " --> pdb=" O PHE I 45 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL I 47 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU I 129 " --> pdb=" O GLU I 157 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL I 159 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.181A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 103 through 105 888 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 135 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7360 1.34 - 1.46: 7340 1.46 - 1.58: 12992 1.58 - 1.70: 660 1.70 - 1.82: 162 Bond restraints: 28514 Sorted by residual: bond pdb=" C ASN B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.337 1.361 -0.024 9.80e-03 1.04e+04 6.24e+00 bond pdb=" CA ILE C 58 " pdb=" CB ILE C 58 " ideal model delta sigma weight residual 1.553 1.539 0.014 7.40e-03 1.83e+04 3.40e+00 bond pdb=" C PHE B 598 " pdb=" N PRO B 599 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.38e+00 bond pdb=" C CYS C 94 " pdb=" N ASN C 95 " ideal model delta sigma weight residual 1.327 1.342 -0.014 9.40e-03 1.13e+04 2.37e+00 bond pdb=" C3' U A 82 " pdb=" O3' U A 82 " ideal model delta sigma weight residual 1.415 1.441 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 28509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 38517 1.87 - 3.74: 1346 3.74 - 5.62: 171 5.62 - 7.49: 18 7.49 - 9.36: 5 Bond angle restraints: 40057 Sorted by residual: angle pdb=" N PHE C 27 " pdb=" CA PHE C 27 " pdb=" C PHE C 27 " ideal model delta sigma weight residual 112.93 106.98 5.95 1.33e+00 5.65e-01 2.00e+01 angle pdb=" N ASN C 95 " pdb=" CA ASN C 95 " pdb=" C ASN C 95 " ideal model delta sigma weight residual 108.19 113.84 -5.65 1.29e+00 6.01e-01 1.92e+01 angle pdb=" C ILE B 202 " pdb=" N LYS B 203 " pdb=" CA LYS B 203 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C3' G A 15 " pdb=" O3' G A 15 " pdb=" P A A 16 " ideal model delta sigma weight residual 119.70 124.71 -5.01 1.20e+00 6.94e-01 1.75e+01 angle pdb=" N HIS K 22 " pdb=" CA HIS K 22 " pdb=" C HIS K 22 " ideal model delta sigma weight residual 112.13 117.65 -5.52 1.37e+00 5.33e-01 1.62e+01 ... (remaining 40052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 15890 34.68 - 69.37: 718 69.37 - 104.05: 56 104.05 - 138.74: 3 138.74 - 173.42: 10 Dihedral angle restraints: 16677 sinusoidal: 9289 harmonic: 7388 Sorted by residual: dihedral pdb=" C4' G A 83 " pdb=" C3' G A 83 " pdb=" C2' G A 83 " pdb=" C1' G A 83 " ideal model delta sinusoidal sigma weight residual 36.34 -36.84 73.18 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' U A 81 " pdb=" C3' U A 81 " pdb=" C2' U A 81 " pdb=" C1' U A 81 " ideal model delta sinusoidal sigma weight residual 36.34 -36.56 72.91 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' A A 97 " pdb=" C3' A A 97 " pdb=" C2' A A 97 " pdb=" C1' A A 97 " ideal model delta sinusoidal sigma weight residual 36.35 -36.53 72.88 1 3.10e+00 1.04e-01 7.05e+02 ... (remaining 16674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4079 0.072 - 0.144: 292 0.144 - 0.216: 7 0.216 - 0.288: 400 0.288 - 0.360: 14 Chirality restraints: 4792 Sorted by residual: chirality pdb=" P A A 16 " pdb=" OP1 A A 16 " pdb=" OP2 A A 16 " pdb=" O5' A A 16 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" P G A 83 " pdb=" OP1 G A 83 " pdb=" OP2 G A 83 " pdb=" O5' G A 83 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" P U A 67 " pdb=" OP1 U A 67 " pdb=" OP2 U A 67 " pdb=" O5' U A 67 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 4789 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 100 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 101 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 118 " 0.018 2.00e-02 2.50e+03 1.42e-02 5.05e+00 pdb=" CG TRP H 118 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP H 118 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 118 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 118 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 118 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 118 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 118 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 118 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 14 " -0.027 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 A A 14 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A A 14 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 14 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 14 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A A 14 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A 14 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 14 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 14 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 14 " 0.003 2.00e-02 2.50e+03 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 180 2.56 - 3.14: 20198 3.14 - 3.73: 43250 3.73 - 4.31: 59736 4.31 - 4.90: 92354 Nonbonded interactions: 215718 Sorted by model distance: nonbonded pdb=" O GLN B 587 " pdb=" OH TYR B 597 " model vdw 1.974 3.040 nonbonded pdb=" O2' A A 31 " pdb=" OP1 G A 264 " model vdw 2.146 3.040 nonbonded pdb=" O2' A A 37 " pdb=" O VAL G 35 " model vdw 2.178 3.040 nonbonded pdb=" O ASP J 89 " pdb=" OG SER J 113 " model vdw 2.196 3.040 nonbonded pdb=" OP1 A A 86 " pdb="MG MG A 401 " model vdw 2.196 2.170 ... (remaining 215713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.720 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 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 : 0.003 0.320 28515 Z= 0.155 Angle : 0.754 9.361 40057 Z= 0.395 Chirality : 0.080 0.360 4792 Planarity : 0.003 0.059 3861 Dihedral : 16.982 173.421 11877 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.15), residues: 2485 helix: -1.14 (0.15), residues: 1016 sheet: -0.99 (0.25), residues: 389 loop : -3.23 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 113 TYR 0.015 0.001 TYR D 136 PHE 0.012 0.001 PHE F 118 TRP 0.038 0.001 TRP H 118 HIS 0.009 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (28514) covalent geometry : angle 0.75445 / 0.39 (40057) hydrogen bonds : bond 0.16412 / 8.40 ( 971) hydrogen bonds : angle 6.73323 / 2.63 ( 2791) metal coordination : bond 0.31983 / 15.99 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 642 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8201 (mmm) cc_final: 0.7964 (mmp) REVERT: B 209 MET cc_start: 0.7356 (mtp) cc_final: 0.7148 (mtt) REVERT: B 362 GLN cc_start: 0.7857 (tt0) cc_final: 0.7297 (tm-30) REVERT: B 603 PRO cc_start: 0.7935 (Cg_endo) cc_final: 0.7644 (Cg_exo) REVERT: D 72 GLN cc_start: 0.7585 (mp10) cc_final: 0.7363 (mp10) REVERT: D 135 GLN cc_start: 0.6657 (mm110) cc_final: 0.6230 (mm-40) REVERT: F 63 ASP cc_start: 0.7633 (p0) cc_final: 0.7371 (p0) REVERT: F 131 GLU cc_start: 0.7125 (pt0) cc_final: 0.6875 (pt0) REVERT: F 132 ARG cc_start: 0.7167 (mpp80) cc_final: 0.6886 (mpp80) REVERT: H 129 ASP cc_start: 0.7361 (t0) cc_final: 0.7146 (t0) REVERT: I 220 ARG cc_start: 0.7268 (mmt180) cc_final: 0.7060 (mpt-90) REVERT: J 223 LYS cc_start: 0.6768 (tptt) cc_final: 0.6295 (ttpp) REVERT: K 28 ASN cc_start: 0.7736 (t0) cc_final: 0.7451 (m-40) REVERT: L 122 ILE cc_start: 0.6252 (mm) cc_final: 0.5756 (mm) outliers start: 2 outliers final: 5 residues processed: 644 average time/residue: 0.6879 time to fit residues: 511.6061 Evaluate side-chains 338 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 333 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 HIS B 201 ASN B 218 ASN B 323 ASN B 335 GLN B 342 ASN B 380 ASN B 570 HIS B 573 ASN B 590 GLN B 665 GLN B 677 ASN B 727 ASN B 774 HIS B 850 GLN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 107 GLN D 99 ASN D 135 GLN D 197 GLN E 50 GLN E 134 ASN F 89 GLN F 153 HIS G 28 GLN G 49 ASN G 58 GLN G 83 GLN G 125 GLN H 128 GLN I 6 ASN I 132 GLN I 213 ASN J 40 HIS K 19 ASN K 108 ASN L 47 GLN L 90 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.169116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.133537 restraints weight = 47561.682| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.41 r_work: 0.4128 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4131 r_free = 0.4131 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4131 r_free = 0.4131 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.4131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28515 Z= 0.182 Angle : 0.972 19.289 40057 Z= 0.414 Chirality : 0.076 1.012 4792 Planarity : 0.005 0.055 3861 Dihedral : 16.206 174.531 6718 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 4.01 % Allowed : 15.90 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.16), residues: 2485 helix: -0.01 (0.16), residues: 1030 sheet: -0.34 (0.25), residues: 396 loop : -2.84 (0.16), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 574 TYR 0.034 0.002 TYR B 597 PHE 0.020 0.002 PHE D 139 TRP 0.054 0.002 TRP H 118 HIS 0.008 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (28514) covalent geometry : angle 0.97172 / 0.41 (40057) hydrogen bonds : bond 0.04477 / 2.30 ( 971) hydrogen bonds : angle 4.61963 / 1.83 ( 2791) metal coordination : bond 0.00189 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 342 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6809 (mtm-85) REVERT: B 112 MET cc_start: 0.8499 (mmm) cc_final: 0.8097 (mmp) REVERT: B 290 SER cc_start: 0.8010 (t) cc_final: 0.7792 (p) REVERT: B 351 LYS cc_start: 0.7765 (tttp) cc_final: 0.7396 (tmtm) REVERT: B 362 GLN cc_start: 0.8245 (tt0) cc_final: 0.7608 (tm-30) REVERT: B 603 PRO cc_start: 0.8100 (Cg_endo) cc_final: 0.7793 (Cg_exo) REVERT: B 612 ASN cc_start: 0.4098 (OUTLIER) cc_final: 0.3853 (t0) REVERT: B 616 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7077 (mptp) REVERT: B 633 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 678 ASP cc_start: 0.5633 (OUTLIER) cc_final: 0.5373 (t0) REVERT: C 45 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8705 (pm20) REVERT: D 73 LEU cc_start: 0.8375 (tp) cc_final: 0.7980 (tp) REVERT: D 76 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.6899 (ttp-110) REVERT: E 22 VAL cc_start: 0.8359 (t) cc_final: 0.7952 (m) REVERT: F 15 ASP cc_start: 0.7118 (t0) cc_final: 0.6796 (t0) REVERT: F 132 ARG cc_start: 0.7458 (mpp80) cc_final: 0.7179 (mpp80) REVERT: G 118 GLU cc_start: 0.6325 (pm20) cc_final: 0.5850 (pm20) REVERT: H 117 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8583 (mm) REVERT: H 129 ASP cc_start: 0.8223 (t0) cc_final: 0.8004 (t0) REVERT: J 1 MET cc_start: 0.7106 (mmm) cc_final: 0.6898 (mmm) REVERT: J 223 LYS cc_start: 0.7250 (tptt) cc_final: 0.6511 (ttpp) REVERT: K 28 ASN cc_start: 0.7971 (t0) cc_final: 0.7659 (m-40) REVERT: L 100 THR cc_start: 0.7691 (t) cc_final: 0.7361 (t) REVERT: L 103 CYS cc_start: 0.7136 (p) cc_final: 0.6755 (p) outliers start: 92 outliers final: 31 residues processed: 400 average time/residue: 0.6662 time to fit residues: 311.1671 Evaluate side-chains 324 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 56 HIS Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 9 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 164 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 230 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN B 273 HIS B 595 GLN B 727 ASN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN E 50 GLN F 106 ASN F 153 HIS H 71 HIS I 213 ASN K 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.159258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.121384 restraints weight = 46942.343| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.43 r_work: 0.3950 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28515 Z= 0.157 Angle : 0.851 12.541 40057 Z= 0.376 Chirality : 0.066 0.785 4792 Planarity : 0.005 0.080 3861 Dihedral : 16.064 179.134 6710 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 4.92 % Allowed : 17.33 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2485 helix: 0.43 (0.16), residues: 1052 sheet: 0.20 (0.26), residues: 372 loop : -2.58 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 36 TYR 0.029 0.002 TYR B 597 PHE 0.021 0.002 PHE B 586 TRP 0.061 0.002 TRP H 118 HIS 0.007 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (28514) covalent geometry : angle 0.85068 / 0.38 (40057) hydrogen bonds : bond 0.04698 / 2.41 ( 971) hydrogen bonds : angle 4.40661 / 1.75 ( 2791) metal coordination : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 331 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.7311 (mmm) cc_final: 0.7089 (mmm) REVERT: B 112 MET cc_start: 0.8585 (mmm) cc_final: 0.8071 (mmp) REVERT: B 191 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7989 (mpt) REVERT: B 290 SER cc_start: 0.8313 (t) cc_final: 0.8090 (p) REVERT: B 323 ASN cc_start: 0.5461 (t0) cc_final: 0.5187 (p0) REVERT: B 362 GLN cc_start: 0.8177 (tt0) cc_final: 0.7634 (tm-30) REVERT: B 370 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6773 (pp) REVERT: B 430 MET cc_start: 0.7975 (ttm) cc_final: 0.7691 (ttp) REVERT: B 466 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7752 (tm130) REVERT: B 539 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8091 (p0) REVERT: B 589 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (mt) REVERT: B 603 PRO cc_start: 0.8186 (Cg_endo) cc_final: 0.7918 (Cg_exo) REVERT: B 612 ASN cc_start: 0.4254 (OUTLIER) cc_final: 0.3945 (t0) REVERT: B 616 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7345 (mptp) REVERT: B 633 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8823 (mp) REVERT: B 678 ASP cc_start: 0.5795 (OUTLIER) cc_final: 0.5455 (m-30) REVERT: B 714 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6714 (tm-30) REVERT: B 811 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7765 (tmtm) REVERT: C 45 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8573 (pm20) REVERT: D 72 GLN cc_start: 0.7969 (mp10) cc_final: 0.7301 (tp-100) REVERT: D 139 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7501 (t80) REVERT: D 206 LYS cc_start: 0.7696 (mttt) cc_final: 0.7399 (mttm) REVERT: D 219 GLU cc_start: 0.4463 (tt0) cc_final: 0.4262 (pt0) REVERT: E 19 ASP cc_start: 0.6554 (t0) cc_final: 0.6339 (t0) REVERT: E 22 VAL cc_start: 0.8439 (t) cc_final: 0.7921 (m) REVERT: F 61 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7398 (mmtt) REVERT: F 125 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6988 (mtp180) REVERT: F 132 ARG cc_start: 0.7277 (mpp80) cc_final: 0.6960 (mpp80) REVERT: I 227 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: J 26 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7389 (tt) REVERT: J 136 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6459 (ppt170) REVERT: J 155 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6718 (ptmt) REVERT: J 196 MET cc_start: 0.6310 (pp-130) cc_final: 0.5939 (ptp) REVERT: J 223 LYS cc_start: 0.7366 (tptt) cc_final: 0.6526 (ttpp) REVERT: K 28 ASN cc_start: 0.8065 (t0) cc_final: 0.7710 (m-40) REVERT: K 29 SER cc_start: 0.7569 (m) cc_final: 0.7228 (p) REVERT: K 56 LYS cc_start: 0.5958 (ptpp) cc_final: 0.5716 (ptpp) REVERT: L 100 THR cc_start: 0.7759 (t) cc_final: 0.7415 (t) REVERT: L 103 CYS cc_start: 0.7200 (p) cc_final: 0.6862 (p) outliers start: 113 outliers final: 30 residues processed: 406 average time/residue: 0.6379 time to fit residues: 304.4536 Evaluate side-chains 316 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 144 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 437 HIS B 505 ASN B 506 ASN B 585 GLN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 GLN B 835 ASN E 50 GLN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN F 153 HIS K 41 HIS K 108 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.155024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.116400 restraints weight = 46588.554| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.43 r_work: 0.3887 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28515 Z= 0.153 Angle : 0.840 11.401 40057 Z= 0.368 Chirality : 0.066 0.747 4792 Planarity : 0.004 0.056 3861 Dihedral : 15.847 176.495 6710 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 4.97 % Allowed : 19.56 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2485 helix: 0.69 (0.16), residues: 1059 sheet: 0.21 (0.26), residues: 393 loop : -2.36 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 626 TYR 0.022 0.002 TYR B 597 PHE 0.024 0.001 PHE B 586 TRP 0.054 0.002 TRP H 118 HIS 0.007 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (28514) covalent geometry : angle 0.84015 / 0.37 (40057) hydrogen bonds : bond 0.04377 / 2.26 ( 971) hydrogen bonds : angle 4.33368 / 1.73 ( 2791) metal coordination : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 305 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6826 (mtm-85) REVERT: B 112 MET cc_start: 0.8570 (mmm) cc_final: 0.8070 (mmp) REVERT: B 191 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8157 (mpt) REVERT: B 205 LEU cc_start: 0.6311 (pt) cc_final: 0.6092 (mt) REVERT: B 362 GLN cc_start: 0.8043 (tt0) cc_final: 0.7542 (tm-30) REVERT: B 370 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7107 (pp) REVERT: B 430 MET cc_start: 0.8058 (ttm) cc_final: 0.7809 (ttp) REVERT: B 461 LYS cc_start: 0.8719 (mttt) cc_final: 0.8516 (mttt) REVERT: B 466 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7699 (tm130) REVERT: B 597 TYR cc_start: 0.5027 (m-80) cc_final: 0.4713 (m-80) REVERT: B 612 ASN cc_start: 0.4468 (OUTLIER) cc_final: 0.4096 (t0) REVERT: B 616 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7912 (mptp) REVERT: B 714 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6676 (tm-30) REVERT: B 811 LYS cc_start: 0.8134 (ptmm) cc_final: 0.7818 (tmtm) REVERT: C 45 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: C 137 LYS cc_start: 0.7401 (tptp) cc_final: 0.6994 (tppp) REVERT: C 140 MET cc_start: 0.5363 (mtm) cc_final: 0.4072 (pmt) REVERT: D 19 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (p0) REVERT: D 72 GLN cc_start: 0.8040 (mp10) cc_final: 0.7496 (tp-100) REVERT: D 135 GLN cc_start: 0.7487 (mm110) cc_final: 0.7158 (mm-40) REVERT: D 158 THR cc_start: 0.8798 (m) cc_final: 0.8541 (p) REVERT: D 206 LYS cc_start: 0.7861 (mttt) cc_final: 0.7403 (mmtp) REVERT: D 219 GLU cc_start: 0.4925 (tt0) cc_final: 0.4276 (mp0) REVERT: E 19 ASP cc_start: 0.6980 (t0) cc_final: 0.6671 (t0) REVERT: E 22 VAL cc_start: 0.8531 (t) cc_final: 0.7986 (m) REVERT: E 42 ASP cc_start: 0.8469 (m-30) cc_final: 0.8210 (t0) REVERT: E 142 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7800 (mppt) REVERT: F 125 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6935 (mtp180) REVERT: F 132 ARG cc_start: 0.7508 (mpp80) cc_final: 0.7137 (mpp80) REVERT: G 89 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7800 (ttpt) REVERT: G 91 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7636 (mt-10) REVERT: G 137 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8052 (mtt-85) REVERT: H 9 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.7231 (p90) REVERT: H 119 LEU cc_start: 0.8440 (mt) cc_final: 0.8151 (mp) REVERT: I 227 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: I 238 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7735 (tm) REVERT: J 26 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7460 (tt) REVERT: J 136 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6533 (ppt170) REVERT: J 196 MET cc_start: 0.6657 (pp-130) cc_final: 0.5938 (mtm) REVERT: J 223 LYS cc_start: 0.7463 (tptt) cc_final: 0.6631 (ttpt) REVERT: K 29 SER cc_start: 0.7641 (m) cc_final: 0.7349 (p) REVERT: K 56 LYS cc_start: 0.6106 (ptpp) cc_final: 0.5725 (ptpp) REVERT: L 84 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6898 (ttm110) REVERT: L 100 THR cc_start: 0.7879 (t) cc_final: 0.7572 (t) REVERT: L 103 CYS cc_start: 0.7561 (p) cc_final: 0.7314 (p) outliers start: 114 outliers final: 42 residues processed: 384 average time/residue: 0.6526 time to fit residues: 292.9713 Evaluate side-chains 320 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 263 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 84 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 254 optimal weight: 0.0070 chunk 221 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 206 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 335 GLN ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 665 GLN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 50 GLN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.157018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.118919 restraints weight = 46799.833| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.44 r_work: 0.3916 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28515 Z= 0.122 Angle : 0.781 11.796 40057 Z= 0.342 Chirality : 0.061 0.697 4792 Planarity : 0.004 0.072 3861 Dihedral : 15.736 176.271 6710 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.88 % Allowed : 22.04 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2485 helix: 0.95 (0.16), residues: 1049 sheet: 0.28 (0.26), residues: 401 loop : -2.30 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 15 TYR 0.022 0.001 TYR K 36 PHE 0.023 0.001 PHE B 586 TRP 0.062 0.001 TRP H 118 HIS 0.016 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (28514) covalent geometry : angle 0.78101 / 0.34 (40057) hydrogen bonds : bond 0.03758 / 1.94 ( 971) hydrogen bonds : angle 4.22682 / 1.69 ( 2791) metal coordination : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 290 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6582 (mtm-85) REVERT: B 112 MET cc_start: 0.8595 (mmm) cc_final: 0.8081 (mmp) REVERT: B 191 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8067 (mpt) REVERT: B 205 LEU cc_start: 0.6342 (pt) cc_final: 0.6099 (mt) REVERT: B 430 MET cc_start: 0.8011 (ttm) cc_final: 0.7749 (ttp) REVERT: B 466 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7765 (tm130) REVERT: B 510 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6675 (tt) REVERT: B 678 ASP cc_start: 0.5817 (OUTLIER) cc_final: 0.5500 (t0) REVERT: B 714 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6653 (tm-30) REVERT: B 811 LYS cc_start: 0.8260 (ptmm) cc_final: 0.7890 (tmtm) REVERT: B 816 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: C 45 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: C 140 MET cc_start: 0.5336 (mtm) cc_final: 0.4217 (pmt) REVERT: D 13 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: D 19 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8105 (p0) REVERT: D 72 GLN cc_start: 0.7860 (mp10) cc_final: 0.7373 (tp-100) REVERT: D 135 GLN cc_start: 0.7618 (mm110) cc_final: 0.7266 (mm-40) REVERT: D 139 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6546 (t80) REVERT: D 206 LYS cc_start: 0.7868 (mttt) cc_final: 0.7562 (mttm) REVERT: D 219 GLU cc_start: 0.4925 (tt0) cc_final: 0.4584 (pt0) REVERT: E 19 ASP cc_start: 0.6959 (t0) cc_final: 0.6676 (t0) REVERT: E 22 VAL cc_start: 0.8536 (t) cc_final: 0.8008 (m) REVERT: E 92 ASP cc_start: 0.7819 (p0) cc_final: 0.7138 (m-30) REVERT: E 131 MET cc_start: 0.7848 (mmt) cc_final: 0.7639 (mmp) REVERT: E 142 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7890 (mppt) REVERT: F 61 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7322 (mmtt) REVERT: F 132 ARG cc_start: 0.7486 (mpp80) cc_final: 0.7109 (mpp80) REVERT: G 53 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: G 89 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7777 (ttpt) REVERT: G 91 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7615 (mt-10) REVERT: G 137 ARG cc_start: 0.8350 (mtt180) cc_final: 0.8088 (mtt-85) REVERT: H 36 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7284 (tm-30) REVERT: H 120 LYS cc_start: 0.8632 (mtpm) cc_final: 0.8163 (mttp) REVERT: I 141 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7524 (mm) REVERT: I 227 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: I 238 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7561 (tm) REVERT: J 78 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6667 (pp) REVERT: J 136 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6446 (ppt170) REVERT: J 196 MET cc_start: 0.6645 (pp-130) cc_final: 0.5972 (mtm) REVERT: K 29 SER cc_start: 0.7633 (m) cc_final: 0.7353 (p) REVERT: K 56 LYS cc_start: 0.6136 (ptpp) cc_final: 0.5766 (ptpp) REVERT: L 103 CYS cc_start: 0.7404 (p) cc_final: 0.7101 (p) outliers start: 89 outliers final: 33 residues processed: 347 average time/residue: 0.6717 time to fit residues: 272.1055 Evaluate side-chains 308 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 170 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 chunk 154 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 508 ASN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 50 GLN F 87 HIS ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS L 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.152614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.113626 restraints weight = 46609.852| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.45 r_work: 0.3838 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28515 Z= 0.156 Angle : 0.830 12.146 40057 Z= 0.366 Chirality : 0.064 0.766 4792 Planarity : 0.004 0.073 3861 Dihedral : 15.783 173.116 6709 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.14 % Allowed : 21.99 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2485 helix: 1.02 (0.16), residues: 1046 sheet: 0.31 (0.26), residues: 386 loop : -2.22 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 15 TYR 0.027 0.002 TYR J 160 PHE 0.029 0.001 PHE K 60 TRP 0.069 0.002 TRP H 118 HIS 0.009 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (28514) covalent geometry : angle 0.83001 / 0.37 (40057) hydrogen bonds : bond 0.04464 / 2.30 ( 971) hydrogen bonds : angle 4.28704 / 1.71 ( 2791) metal coordination : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 300 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6693 (mtm-85) REVERT: B 112 MET cc_start: 0.8671 (mmm) cc_final: 0.8191 (mmp) REVERT: B 145 LYS cc_start: 0.7704 (ptmt) cc_final: 0.7338 (mmtm) REVERT: B 191 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8068 (mpt) REVERT: B 430 MET cc_start: 0.8174 (ttm) cc_final: 0.7900 (ttp) REVERT: B 461 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8338 (mttt) REVERT: B 466 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7827 (tm130) REVERT: B 510 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6799 (tt) REVERT: B 612 ASN cc_start: 0.5018 (OUTLIER) cc_final: 0.4794 (t0) REVERT: B 678 ASP cc_start: 0.5880 (OUTLIER) cc_final: 0.5475 (m-30) REVERT: B 684 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6102 (mmm) REVERT: B 714 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6668 (tm-30) REVERT: B 811 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8028 (tmtm) REVERT: B 816 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: C 45 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: C 117 MET cc_start: 0.7867 (mpm) cc_final: 0.7004 (mtp) REVERT: C 140 MET cc_start: 0.5391 (mtm) cc_final: 0.4109 (pmt) REVERT: D 19 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8017 (p0) REVERT: D 72 GLN cc_start: 0.7969 (mp10) cc_final: 0.7522 (tp-100) REVERT: D 76 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6940 (ttp-110) REVERT: D 139 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7713 (t80) REVERT: D 206 LYS cc_start: 0.7904 (mttt) cc_final: 0.7637 (mttm) REVERT: E 19 ASP cc_start: 0.7235 (t0) cc_final: 0.6958 (t0) REVERT: E 22 VAL cc_start: 0.8446 (t) cc_final: 0.7898 (m) REVERT: E 69 ASN cc_start: 0.7930 (t0) cc_final: 0.7706 (t0) REVERT: E 92 ASP cc_start: 0.7880 (p0) cc_final: 0.7372 (m-30) REVERT: E 108 ASP cc_start: 0.7697 (p0) cc_final: 0.7394 (p0) REVERT: E 131 MET cc_start: 0.7867 (mmt) cc_final: 0.7644 (mmp) REVERT: F 125 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7075 (mtp180) REVERT: F 132 ARG cc_start: 0.7452 (mpp80) cc_final: 0.7020 (mpp80) REVERT: G 28 GLN cc_start: 0.8562 (mt0) cc_final: 0.8339 (mt0) REVERT: G 89 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7853 (ttpt) REVERT: H 9 TRP cc_start: 0.7343 (p90) cc_final: 0.6450 (p90) REVERT: H 25 ASP cc_start: 0.8423 (m-30) cc_final: 0.7970 (p0) REVERT: H 36 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7245 (tm-30) REVERT: H 123 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.5914 (tpt) REVERT: I 58 LYS cc_start: 0.8475 (mppt) cc_final: 0.8238 (mppt) REVERT: I 140 PHE cc_start: 0.7261 (t80) cc_final: 0.6880 (t80) REVERT: I 168 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8134 (mp10) REVERT: I 196 MET cc_start: 0.7710 (pmm) cc_final: 0.7454 (ppp) REVERT: I 227 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: J 136 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6545 (ppt170) REVERT: J 239 ARG cc_start: 0.7450 (ttp80) cc_final: 0.6682 (tmm-80) REVERT: K 28 ASN cc_start: 0.8101 (t0) cc_final: 0.7200 (p0) REVERT: K 29 SER cc_start: 0.7664 (m) cc_final: 0.7331 (p) REVERT: K 56 LYS cc_start: 0.6150 (ptpp) cc_final: 0.5846 (ptpp) REVERT: L 69 LYS cc_start: 0.6975 (pttt) cc_final: 0.6730 (pptt) REVERT: L 100 THR cc_start: 0.7913 (t) cc_final: 0.7624 (t) REVERT: L 103 CYS cc_start: 0.7557 (p) cc_final: 0.7102 (p) outliers start: 95 outliers final: 44 residues processed: 362 average time/residue: 0.6314 time to fit residues: 268.3808 Evaluate side-chains 321 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 201 CYS Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 153 optimal weight: 0.9980 chunk 211 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 331 GLN B 505 ASN B 508 ASN D 126 HIS F 52 ASN F 153 HIS ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN K 48 GLN L 13 GLN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.152835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114124 restraints weight = 46407.909| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.44 r_work: 0.3851 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28515 Z= 0.141 Angle : 0.809 12.629 40057 Z= 0.356 Chirality : 0.063 0.748 4792 Planarity : 0.004 0.077 3861 Dihedral : 15.779 172.649 6709 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.70 % Allowed : 23.48 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2485 helix: 1.05 (0.17), residues: 1049 sheet: 0.35 (0.26), residues: 398 loop : -2.15 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 15 TYR 0.025 0.002 TYR K 36 PHE 0.028 0.001 PHE K 60 TRP 0.079 0.002 TRP H 118 HIS 0.012 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (28514) covalent geometry : angle 0.80897 / 0.36 (40057) hydrogen bonds : bond 0.04113 / 2.13 ( 971) hydrogen bonds : angle 4.25276 / 1.70 ( 2791) metal coordination : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6562 (mtm-85) REVERT: B 112 MET cc_start: 0.8608 (mmm) cc_final: 0.8106 (mmp) REVERT: B 145 LYS cc_start: 0.7722 (ptmt) cc_final: 0.7350 (mmtm) REVERT: B 191 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8116 (mpt) REVERT: B 193 LYS cc_start: 0.7993 (ptpp) cc_final: 0.7599 (ptpp) REVERT: B 430 MET cc_start: 0.8181 (ttm) cc_final: 0.7949 (ttp) REVERT: B 461 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8201 (mttt) REVERT: B 466 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7766 (tm130) REVERT: B 479 HIS cc_start: 0.7556 (t-90) cc_final: 0.7338 (t-90) REVERT: B 510 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6793 (tt) REVERT: B 597 TYR cc_start: 0.5781 (t80) cc_final: 0.5388 (t80) REVERT: B 678 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.5393 (m-30) REVERT: B 684 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6215 (mmm) REVERT: B 714 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6653 (tm-30) REVERT: B 811 LYS cc_start: 0.8352 (ptmm) cc_final: 0.7971 (tmtm) REVERT: C 45 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: C 117 MET cc_start: 0.7930 (mpm) cc_final: 0.7100 (mtp) REVERT: C 140 MET cc_start: 0.5333 (mtm) cc_final: 0.4108 (pmt) REVERT: D 19 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8071 (p0) REVERT: D 72 GLN cc_start: 0.7989 (mp10) cc_final: 0.7521 (tp-100) REVERT: D 206 LYS cc_start: 0.7883 (mttt) cc_final: 0.7598 (mttm) REVERT: E 69 ASN cc_start: 0.7904 (t0) cc_final: 0.7679 (t0) REVERT: E 92 ASP cc_start: 0.7884 (p0) cc_final: 0.7254 (m-30) REVERT: E 131 MET cc_start: 0.7866 (mmt) cc_final: 0.7648 (mmp) REVERT: F 125 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6904 (mtp180) REVERT: F 131 GLU cc_start: 0.8259 (pt0) cc_final: 0.7547 (pp20) REVERT: F 132 ARG cc_start: 0.7454 (mpp80) cc_final: 0.6859 (mpp80) REVERT: G 89 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7860 (ttpt) REVERT: G 91 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7613 (mt-10) REVERT: H 9 TRP cc_start: 0.7433 (OUTLIER) cc_final: 0.6347 (p90) REVERT: H 25 ASP cc_start: 0.8359 (m-30) cc_final: 0.7943 (p0) REVERT: H 36 GLN cc_start: 0.7509 (tm-30) cc_final: 0.7183 (tm-30) REVERT: I 196 MET cc_start: 0.7749 (pmm) cc_final: 0.7501 (ppp) REVERT: I 227 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: J 136 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6577 (ppt170) REVERT: J 225 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6199 (mtt) REVERT: K 28 ASN cc_start: 0.7970 (t0) cc_final: 0.7413 (p0) REVERT: K 29 SER cc_start: 0.7514 (m) cc_final: 0.7294 (p) REVERT: K 56 LYS cc_start: 0.6206 (ptpp) cc_final: 0.5877 (ptpp) REVERT: K 89 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7189 (pt0) REVERT: L 84 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6841 (ttm170) REVERT: L 100 THR cc_start: 0.7866 (t) cc_final: 0.7580 (t) REVERT: L 103 CYS cc_start: 0.7455 (p) cc_final: 0.6967 (p) outliers start: 85 outliers final: 40 residues processed: 347 average time/residue: 0.6422 time to fit residues: 261.0938 Evaluate side-chains 316 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 84 ARG Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 192 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 331 GLN ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 505 ASN B 508 ASN ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 50 GLN F 37 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS G 28 GLN H 27 HIS ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN L 75 GLN L 111 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.148789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.109492 restraints weight = 46889.328| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.40 r_work: 0.3720 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28515 Z= 0.176 Angle : 0.867 14.055 40057 Z= 0.384 Chirality : 0.066 0.817 4792 Planarity : 0.005 0.084 3861 Dihedral : 15.884 175.574 6709 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.96 % Allowed : 24.09 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2485 helix: 0.94 (0.17), residues: 1050 sheet: 0.35 (0.26), residues: 394 loop : -2.10 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 15 TYR 0.026 0.002 TYR J 160 PHE 0.049 0.002 PHE L 127 TRP 0.086 0.002 TRP H 118 HIS 0.009 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (28514) covalent geometry : angle 0.86670 / 0.38 (40057) hydrogen bonds : bond 0.04812 / 2.48 ( 971) hydrogen bonds : angle 4.39681 / 1.77 ( 2791) metal coordination : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 279 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6814 (mtm-85) REVERT: B 112 MET cc_start: 0.8678 (mmm) cc_final: 0.8231 (mmp) REVERT: B 145 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7531 (mmtm) REVERT: B 191 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8083 (mpt) REVERT: B 430 MET cc_start: 0.8235 (ttm) cc_final: 0.7983 (ttp) REVERT: B 461 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8199 (mttt) REVERT: B 466 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7844 (mm-40) REVERT: B 479 HIS cc_start: 0.7579 (t-90) cc_final: 0.7378 (t-90) REVERT: B 510 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6660 (tt) REVERT: B 597 TYR cc_start: 0.5821 (t80) cc_final: 0.5411 (t80) REVERT: B 678 ASP cc_start: 0.5899 (OUTLIER) cc_final: 0.5508 (m-30) REVERT: B 684 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6165 (mmm) REVERT: B 714 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6644 (tm-30) REVERT: B 811 LYS cc_start: 0.8345 (ptmm) cc_final: 0.8034 (tmtm) REVERT: C 68 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8332 (mm) REVERT: C 117 MET cc_start: 0.7932 (mpm) cc_final: 0.7207 (mtp) REVERT: C 140 MET cc_start: 0.5602 (mtm) cc_final: 0.4775 (pmt) REVERT: D 19 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8025 (p0) REVERT: D 72 GLN cc_start: 0.8026 (mp10) cc_final: 0.7528 (tp-100) REVERT: D 269 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6782 (ttp-170) REVERT: E 69 ASN cc_start: 0.7876 (t0) cc_final: 0.7670 (t0) REVERT: E 92 ASP cc_start: 0.7867 (p0) cc_final: 0.7347 (m-30) REVERT: E 131 MET cc_start: 0.7880 (mmt) cc_final: 0.7656 (mmp) REVERT: F 125 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.7011 (mtp180) REVERT: F 131 GLU cc_start: 0.8290 (pt0) cc_final: 0.7468 (pp20) REVERT: F 132 ARG cc_start: 0.7455 (mpp80) cc_final: 0.6835 (mpp80) REVERT: G 89 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7856 (ttpt) REVERT: G 91 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7602 (mt-10) REVERT: H 9 TRP cc_start: 0.7461 (OUTLIER) cc_final: 0.6347 (p90) REVERT: H 25 ASP cc_start: 0.8388 (m-30) cc_final: 0.8023 (p0) REVERT: H 36 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7183 (tm-30) REVERT: I 71 GLU cc_start: 0.8447 (pp20) cc_final: 0.7919 (tm-30) REVERT: I 136 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8258 (mmm-85) REVERT: I 140 PHE cc_start: 0.7342 (t80) cc_final: 0.6916 (t80) REVERT: I 168 GLN cc_start: 0.8788 (tp-100) cc_final: 0.7965 (mp10) REVERT: I 196 MET cc_start: 0.7874 (pmm) cc_final: 0.7619 (ppp) REVERT: J 78 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6916 (pp) REVERT: J 136 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6664 (ppt170) REVERT: J 225 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6374 (mtp) REVERT: K 56 LYS cc_start: 0.6248 (ptpp) cc_final: 0.5903 (ptpp) REVERT: L 84 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6802 (ttm170) REVERT: L 100 THR cc_start: 0.7867 (t) cc_final: 0.7572 (t) REVERT: L 103 CYS cc_start: 0.7387 (p) cc_final: 0.7002 (p) REVERT: L 111 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6800 (m110) outliers start: 91 outliers final: 41 residues processed: 344 average time/residue: 0.6665 time to fit residues: 267.7890 Evaluate side-chains 317 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 84 ARG Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 111 ASN Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 16 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 222 optimal weight: 0.4980 chunk 180 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 508 ASN B 665 GLN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 50 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS G 28 GLN H 27 HIS L 111 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.148387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.109202 restraints weight = 46572.600| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.38 r_work: 0.3721 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28515 Z= 0.172 Angle : 0.879 15.366 40057 Z= 0.391 Chirality : 0.066 0.836 4792 Planarity : 0.005 0.085 3861 Dihedral : 15.899 176.040 6709 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.61 % Allowed : 25.22 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2485 helix: 0.98 (0.17), residues: 1044 sheet: 0.32 (0.26), residues: 392 loop : -2.13 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 15 TYR 0.024 0.002 TYR K 36 PHE 0.017 0.001 PHE L 127 TRP 0.087 0.002 TRP H 118 HIS 0.009 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (28514) covalent geometry : angle 0.87913 / 0.39 (40057) hydrogen bonds : bond 0.04712 / 2.43 ( 971) hydrogen bonds : angle 4.43736 / 1.78 ( 2791) metal coordination : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 277 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6721 (mtm-85) REVERT: B 112 MET cc_start: 0.8654 (mmm) cc_final: 0.8202 (mmp) REVERT: B 145 LYS cc_start: 0.7936 (ptmt) cc_final: 0.7556 (mmtm) REVERT: B 191 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8169 (mpt) REVERT: B 430 MET cc_start: 0.8218 (ttm) cc_final: 0.7956 (ttp) REVERT: B 461 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8173 (mttt) REVERT: B 466 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7904 (mm-40) REVERT: B 510 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6641 (tt) REVERT: B 597 TYR cc_start: 0.5852 (t80) cc_final: 0.5545 (t80) REVERT: B 678 ASP cc_start: 0.5870 (OUTLIER) cc_final: 0.5502 (m-30) REVERT: B 684 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6190 (mmm) REVERT: B 714 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6660 (tm-30) REVERT: B 811 LYS cc_start: 0.8361 (ptmm) cc_final: 0.8044 (tmtm) REVERT: C 45 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: C 68 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8357 (mm) REVERT: C 117 MET cc_start: 0.7930 (mpm) cc_final: 0.7177 (mtp) REVERT: C 140 MET cc_start: 0.5593 (mtm) cc_final: 0.4744 (pmt) REVERT: D 19 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8016 (p0) REVERT: D 72 GLN cc_start: 0.8024 (mp10) cc_final: 0.7383 (tp-100) REVERT: E 69 ASN cc_start: 0.7881 (t0) cc_final: 0.7669 (t0) REVERT: E 131 MET cc_start: 0.7871 (mmt) cc_final: 0.7648 (mmp) REVERT: E 133 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8051 (ttt90) REVERT: F 63 ASP cc_start: 0.8326 (p0) cc_final: 0.8072 (p0) REVERT: F 125 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6854 (mtp180) REVERT: F 131 GLU cc_start: 0.8278 (pt0) cc_final: 0.7464 (pp20) REVERT: F 132 ARG cc_start: 0.7478 (mpp80) cc_final: 0.6802 (mpp80) REVERT: G 57 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8203 (tptp) REVERT: G 89 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7841 (ttpt) REVERT: G 91 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7624 (mt-10) REVERT: H 9 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.6347 (p90) REVERT: H 25 ASP cc_start: 0.8227 (m-30) cc_final: 0.7998 (p0) REVERT: H 36 GLN cc_start: 0.7476 (tm-30) cc_final: 0.7196 (tm-30) REVERT: H 43 LYS cc_start: 0.7347 (tppt) cc_final: 0.7078 (tptp) REVERT: H 123 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.5993 (tpt) REVERT: I 73 MET cc_start: 0.8229 (mtm) cc_final: 0.8006 (mtp) REVERT: I 140 PHE cc_start: 0.7341 (t80) cc_final: 0.6969 (t80) REVERT: I 168 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8040 (mp10) REVERT: I 196 MET cc_start: 0.7784 (pmm) cc_final: 0.7569 (ppp) REVERT: J 136 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6657 (ppt170) REVERT: J 225 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6604 (mtt) REVERT: K 56 LYS cc_start: 0.6162 (ptpp) cc_final: 0.5823 (ptpp) REVERT: K 89 GLU cc_start: 0.7022 (pt0) cc_final: 0.6634 (pt0) REVERT: L 103 CYS cc_start: 0.7361 (p) cc_final: 0.6945 (p) REVERT: L 111 ASN cc_start: 0.7120 (OUTLIER) cc_final: 0.6860 (m110) REVERT: L 123 ASN cc_start: 0.7989 (m110) cc_final: 0.7717 (m-40) outliers start: 83 outliers final: 49 residues processed: 337 average time/residue: 0.6438 time to fit residues: 253.7125 Evaluate side-chains 328 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 225 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 111 ASN Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 46 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 chunk 212 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 508 ASN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS E 50 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS G 28 GLN G 81 HIS H 27 HIS ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN L 39 ASN L 111 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.146586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.107230 restraints weight = 46817.165| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.39 r_work: 0.3688 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28515 Z= 0.187 Angle : 0.910 17.200 40057 Z= 0.406 Chirality : 0.068 0.877 4792 Planarity : 0.005 0.091 3861 Dihedral : 15.959 178.701 6709 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.31 % Allowed : 26.13 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2485 helix: 0.86 (0.16), residues: 1041 sheet: 0.25 (0.26), residues: 393 loop : -2.08 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 15 TYR 0.025 0.002 TYR K 36 PHE 0.014 0.002 PHE C 166 TRP 0.092 0.002 TRP H 118 HIS 0.006 0.001 HIS B 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (28514) covalent geometry : angle 0.91001 / 0.41 (40057) hydrogen bonds : bond 0.05059 / 2.61 ( 971) hydrogen bonds : angle 4.50602 / 1.81 ( 2791) metal coordination : bond 0.00097 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 269 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6655 (mtm-85) REVERT: B 112 MET cc_start: 0.8622 (mmm) cc_final: 0.8187 (mmp) REVERT: B 145 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7720 (mmtm) REVERT: B 191 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8187 (mpt) REVERT: B 234 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6568 (pt0) REVERT: B 430 MET cc_start: 0.8238 (ttm) cc_final: 0.7964 (ttp) REVERT: B 461 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8173 (mttt) REVERT: B 466 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7990 (mm-40) REVERT: B 510 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6662 (tt) REVERT: B 597 TYR cc_start: 0.6012 (t80) cc_final: 0.5649 (t80) REVERT: B 678 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5584 (m-30) REVERT: B 684 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6192 (mmm) REVERT: B 714 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6654 (tm-30) REVERT: B 811 LYS cc_start: 0.8342 (ptmm) cc_final: 0.8029 (tmtm) REVERT: C 45 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: C 68 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8005 (mm) REVERT: C 117 MET cc_start: 0.7938 (mpm) cc_final: 0.7236 (mtp) REVERT: C 140 MET cc_start: 0.5646 (mtm) cc_final: 0.4792 (pmt) REVERT: D 19 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8021 (p0) REVERT: D 269 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6759 (ttp-170) REVERT: E 69 ASN cc_start: 0.7861 (t0) cc_final: 0.7646 (t0) REVERT: E 131 MET cc_start: 0.7902 (mmt) cc_final: 0.7678 (mmp) REVERT: E 133 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8015 (ttt90) REVERT: F 63 ASP cc_start: 0.8366 (p0) cc_final: 0.8121 (p0) REVERT: F 125 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6938 (mtp180) REVERT: F 131 GLU cc_start: 0.8249 (pt0) cc_final: 0.7460 (pp20) REVERT: F 132 ARG cc_start: 0.7598 (mpp80) cc_final: 0.6958 (mpp80) REVERT: G 89 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7874 (ttpt) REVERT: G 91 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7830 (mt-10) REVERT: H 9 TRP cc_start: 0.7420 (OUTLIER) cc_final: 0.6457 (p90) REVERT: H 25 ASP cc_start: 0.8241 (m-30) cc_final: 0.7971 (p0) REVERT: H 36 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7189 (tm-30) REVERT: H 43 LYS cc_start: 0.7456 (tppt) cc_final: 0.7195 (tptp) REVERT: H 123 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.5916 (tpt) REVERT: I 73 MET cc_start: 0.8294 (mtm) cc_final: 0.8044 (mtp) REVERT: I 140 PHE cc_start: 0.7297 (t80) cc_final: 0.6904 (t80) REVERT: I 168 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8121 (mp10) REVERT: K 56 LYS cc_start: 0.6292 (ptpp) cc_final: 0.5937 (ptpp) REVERT: L 103 CYS cc_start: 0.7541 (p) cc_final: 0.7122 (p) outliers start: 76 outliers final: 44 residues processed: 324 average time/residue: 0.6454 time to fit residues: 245.4798 Evaluate side-chains 316 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 257 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 23 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 130 optimal weight: 0.0060 chunk 216 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.0040 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 508 ASN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN E 50 GLN F 37 ASN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.146875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.107615 restraints weight = 46172.645| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.39 r_work: 0.3687 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28515 Z= 0.174 Angle : 0.897 17.052 40057 Z= 0.400 Chirality : 0.067 0.864 4792 Planarity : 0.005 0.089 3861 Dihedral : 15.959 177.925 6709 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.01 % Allowed : 26.35 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2485 helix: 0.94 (0.17), residues: 1035 sheet: 0.25 (0.25), residues: 400 loop : -2.09 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 116 TYR 0.025 0.002 TYR K 36 PHE 0.019 0.002 PHE K 60 TRP 0.094 0.002 TRP H 118 HIS 0.032 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (28514) covalent geometry : angle 0.89682 / 0.40 (40057) hydrogen bonds : bond 0.04778 / 2.46 ( 971) hydrogen bonds : angle 4.48168 / 1.80 ( 2791) metal coordination : bond 0.00053 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16541.95 seconds wall clock time: 280 minutes 56.57 seconds (16856.57 seconds total)