Starting phenix.real_space_refine on Mon Aug 25 12:31:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yha_39286/08_2025/8yha_39286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yha_39286/08_2025/8yha_39286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yha_39286/08_2025/8yha_39286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yha_39286/08_2025/8yha_39286.map" model { file = "/net/cci-nas-00/data/ceres_data/8yha_39286/08_2025/8yha_39286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yha_39286/08_2025/8yha_39286.cif" } resolution = 3.4 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 107 5.49 5 S 115 5.16 5 C 17717 2.51 5 N 5006 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28503 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2756 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2174 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 20, 'TRANS': 247} Chain: "C" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1303 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 23, 'rna3p_pyr': 17} Link IDs: {'rna2p': 20, 'rna3p': 40} Chain: "D" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2792 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 1 Chain: "E" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2923 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 13, 'TRANS': 361} Chain: "F" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2897 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain: "G" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2882 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain: "H" Number of atoms: 2891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2891 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 13, 'TRANS': 357} Chain: "I" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2056 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 12, 'TRANS': 253} Chain breaks: 2 Chain: "J" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3521 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "K" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1356 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain: "T" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 950 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" 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 2139 SG CYS A 298 47.323 47.090 74.479 1.00 76.41 S ATOM 2160 SG CYS A 301 45.223 48.903 71.837 1.00 71.26 S ATOM 2376 SG CYS A 329 48.864 49.639 71.944 1.00 75.96 S ATOM 2401 SG CYS A 332 46.750 50.817 74.794 1.00 67.61 S ATOM 23794 SG CYS J 215 96.003 47.807 159.675 1.00 72.67 S ATOM 23814 SG CYS J 218 95.359 51.115 157.940 1.00 71.25 S ATOM 24533 SG CYS J 311 92.570 48.652 158.301 1.00 68.39 S ATOM 24551 SG CYS J 314 95.584 47.876 155.937 1.00 57.69 S Time building chain proxies: 6.75, per 1000 atoms: 0.24 Number of scatterers: 28503 At special positions: 0 Unit cell: (134.3, 143.65, 189.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 115 16.00 P 107 15.00 O 5556 8.00 N 5006 7.00 C 17717 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 301 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 332 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 329 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 298 " pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 215 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 218 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 311 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 314 " Number of angles added : 12 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6220 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 37 sheets defined 38.6% alpha, 19.4% beta 29 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.805A pdb=" N ALA A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.924A pdb=" N LYS A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 4.066A pdb=" N VAL A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.968A pdb=" N ALA A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'B' and resid 19 through 27 removed outlier: 3.965A pdb=" N ASN B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 37 Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.818A pdb=" N ASP B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.500A pdb=" N PHE B 60 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.502A pdb=" N CYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 96' Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.873A pdb=" N LYS B 178 " --> pdb=" O TRP B 174 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 240 through 251 removed outlier: 3.788A pdb=" N PHE B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.899A pdb=" N ARG D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 78 through 89 removed outlier: 3.557A pdb=" N LEU D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 107 through 117 removed outlier: 4.339A pdb=" N ASP D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 removed outlier: 3.637A pdb=" N VAL D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 233 through 250 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.624A pdb=" N VAL D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.505A pdb=" N LEU E 55 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 removed outlier: 3.632A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 88 removed outlier: 3.575A pdb=" N LYS E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS E 88 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 117 Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'E' and resid 139 through 146 removed outlier: 3.796A pdb=" N LEU E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 234 through 250 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.590A pdb=" N VAL E 285 " --> pdb=" O ASN E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 315 Processing helix chain 'E' and resid 329 through 332 Processing helix chain 'E' and resid 349 through 363 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.517A pdb=" N LEU F 56 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 76 through 88 removed outlier: 3.879A pdb=" N LYS F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 121 through 135 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 249 Processing helix chain 'F' and resid 279 through 286 removed outlier: 4.524A pdb=" N ASN F 282 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE F 284 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG F 286 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 315 removed outlier: 3.526A pdb=" N GLN F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 332 Processing helix chain 'F' and resid 349 through 361 removed outlier: 3.527A pdb=" N ILE F 361 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 52 through 56 removed outlier: 3.560A pdb=" N LEU G 56 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.797A pdb=" N LEU G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 Processing helix chain 'G' and resid 107 through 117 Processing helix chain 'G' and resid 121 through 135 Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 233 through 250 Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.532A pdb=" N PHE G 284 " --> pdb=" O ALA G 281 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 315 removed outlier: 3.618A pdb=" N GLN G 299 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 332 Processing helix chain 'G' and resid 350 through 362 Processing helix chain 'G' and resid 365 through 370 removed outlier: 3.841A pdb=" N GLN G 370 " --> pdb=" O TRP G 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 52 through 56 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.995A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 107 through 117 removed outlier: 3.728A pdb=" N ASP H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.801A pdb=" N ALA H 125 " --> pdb=" O GLY H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 280 through 285 removed outlier: 3.532A pdb=" N PHE H 284 " --> pdb=" O ALA H 281 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 285 " --> pdb=" O ASN H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 315 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 363 Processing helix chain 'H' and resid 365 through 370 Processing helix chain 'I' and resid 38 through 48 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 139 through 145 Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 234 through 250 Processing helix chain 'I' and resid 280 through 286 removed outlier: 4.493A pdb=" N ARG I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 313 Processing helix chain 'I' and resid 329 through 332 Processing helix chain 'I' and resid 349 through 362 Processing helix chain 'J' and resid 103 through 110 Processing helix chain 'J' and resid 120 through 143 Processing helix chain 'J' and resid 155 through 163 removed outlier: 3.534A pdb=" N TRP J 159 " --> pdb=" O SER J 155 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN J 163 " --> pdb=" O TRP J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 192 removed outlier: 3.535A pdb=" N ILE J 192 " --> pdb=" O THR J 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 189 through 192' Processing helix chain 'J' and resid 215 through 224 Processing helix chain 'J' and resid 255 through 263 Processing helix chain 'J' and resid 287 through 293 Processing helix chain 'J' and resid 369 through 373 removed outlier: 4.386A pdb=" N TYR J 372 " --> pdb=" O ARG J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 381 removed outlier: 4.035A pdb=" N ALA J 381 " --> pdb=" O TYR J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 427 Processing helix chain 'J' and resid 427 through 437 removed outlier: 3.707A pdb=" N ALA J 431 " --> pdb=" O ASN J 427 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN J 433 " --> pdb=" O ALA J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 465 removed outlier: 4.213A pdb=" N ALA J 454 " --> pdb=" O THR J 450 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE J 456 " --> pdb=" O GLN J 452 " (cutoff:3.500A) Proline residue: J 458 - end of helix Processing helix chain 'J' and resid 467 through 474 Processing helix chain 'J' and resid 478 through 483 Processing helix chain 'J' and resid 484 through 498 removed outlier: 3.879A pdb=" N GLU J 488 " --> pdb=" O THR J 484 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU J 489 " --> pdb=" O GLU J 485 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS J 492 " --> pdb=" O GLU J 488 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 493 " --> pdb=" O LEU J 489 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR J 495 " --> pdb=" O THR J 491 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER J 496 " --> pdb=" O LYS J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 514 removed outlier: 4.041A pdb=" N SER J 514 " --> pdb=" O GLY J 510 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 Processing helix chain 'K' and resid 16 through 25 removed outlier: 3.598A pdb=" N LEU K 20 " --> pdb=" O LYS K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 52 removed outlier: 3.672A pdb=" N PHE K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) Proline residue: K 47 - end of helix removed outlier: 3.722A pdb=" N GLN K 50 " --> pdb=" O TRP K 46 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS K 51 " --> pdb=" O PRO K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 71 Processing helix chain 'K' and resid 80 through 91 removed outlier: 3.915A pdb=" N LYS K 91 " --> pdb=" O GLY K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 107 removed outlier: 3.572A pdb=" N ARG K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 111 removed outlier: 3.657A pdb=" N LEU K 111 " --> pdb=" O LEU K 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 108 through 111' Processing helix chain 'K' and resid 112 through 115 Processing helix chain 'K' and resid 116 through 130 removed outlier: 3.900A pdb=" N ILE K 123 " --> pdb=" O PRO K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 149 through 166 removed outlier: 3.526A pdb=" N LYS K 153 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 17 removed outlier: 6.651A pdb=" N THR A 7 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN A 142 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 9 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 140 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG A 11 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 138 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU A 13 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER A 136 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA A 15 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 7.304A pdb=" N ARG A 29 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LEU A 132 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A 136 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET A 68 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ARG A 74 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N ILE A 207 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 243 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 232 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.287A pdb=" N LEU A 195 " --> pdb=" O SER A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 73 removed outlier: 4.837A pdb=" N ALA B 80 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 110 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 108 " --> pdb=" O ARG B 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 184 through 186 removed outlier: 3.709A pdb=" N GLN B 193 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU B 233 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU B 191 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 186 removed outlier: 3.775A pdb=" N SER B 264 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 171 through 173 removed outlier: 3.846A pdb=" N ILE D 323 " --> pdb=" O PHE D 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 26 through 29 Processing sheet with id=AB1, first strand: chain 'D' and resid 59 through 61 Processing sheet with id=AB2, first strand: chain 'D' and resid 147 through 148 Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 28 removed outlier: 6.033A pdb=" N SER E 35 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 177 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY E 268 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE E 323 " --> pdb=" O PHE E 273 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY E 324 " --> pdb=" O ARG E 345 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE E 347 " --> pdb=" O GLY E 324 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP E 326 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 190 Processing sheet with id=AB6, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.577A pdb=" N CYS F 27 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR F 218 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA F 176 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR F 216 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER F 178 " --> pdb=" O CYS F 214 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS F 214 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA F 191 " --> pdb=" O GLY F 203 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE F 205 " --> pdb=" O PHE F 189 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE F 189 " --> pdb=" O ILE F 205 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU F 207 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP F 187 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET F 209 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU F 185 " --> pdb=" O MET F 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.577A pdb=" N CYS F 27 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR F 218 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA F 176 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR F 216 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER F 178 " --> pdb=" O CYS F 214 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS F 214 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA F 211 " --> pdb=" O PRO F 13 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE F 323 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 345 " --> pdb=" O GLY F 324 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'F' and resid 92 through 93 removed outlier: 3.611A pdb=" N ASN F 96 " --> pdb=" O LYS F 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 147 through 148 Processing sheet with id=AC2, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.597A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 177 " --> pdb=" O TYR G 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.597A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 177 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE G 323 " --> pdb=" O PHE G 273 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLY G 324 " --> pdb=" O ARG G 345 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE G 347 " --> pdb=" O GLY G 324 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP G 326 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 58 through 61 Processing sheet with id=AC5, first strand: chain 'G' and resid 185 through 190 Processing sheet with id=AC6, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.705A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.705A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLY H 324 " --> pdb=" O ARG H 345 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE H 347 " --> pdb=" O GLY H 324 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TRP H 326 " --> pdb=" O ILE H 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 58 through 61 Processing sheet with id=AC9, first strand: chain 'H' and resid 147 through 148 Processing sheet with id=AD1, first strand: chain 'H' and resid 185 through 191 Processing sheet with id=AD2, first strand: chain 'I' and resid 26 through 29 removed outlier: 5.791A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 26 through 29 removed outlier: 5.791A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY I 268 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 323 " --> pdb=" O PHE I 273 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ILE I 347 " --> pdb=" O GLY I 324 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP I 326 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 184 through 191 removed outlier: 4.359A pdb=" N HIS I 204 " --> pdb=" O ALA I 191 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 99 through 102 Processing sheet with id=AD6, first strand: chain 'J' and resid 185 through 187 Processing sheet with id=AD7, first strand: chain 'J' and resid 305 through 310 removed outlier: 4.640A pdb=" N GLU J 319 " --> pdb=" O GLY J 307 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA J 309 " --> pdb=" O PRO J 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 388 through 390 Processing sheet with id=AD9, first strand: chain 'J' and resid 393 through 397 Processing sheet with id=AE1, first strand: chain 'K' and resid 74 through 75 removed outlier: 5.698A pdb=" N GLU K 74 " --> pdb=" O LEU K 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 1116 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 2.71 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: 8183 1.34 - 1.46: 6111 1.46 - 1.58: 14675 1.58 - 1.70: 213 1.70 - 1.82: 171 Bond restraints: 29353 Sorted by residual: bond pdb=" C SER F 12 " pdb=" N PRO F 13 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.09e+00 bond pdb=" CB LYS D 80 " pdb=" CG LYS D 80 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB GLU A 228 " pdb=" CG GLU A 228 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" O5' C C 47 " pdb=" C5' C C 47 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.65e+00 bond pdb=" O5' G C 8 " pdb=" C5' G C 8 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.61e+00 ... (remaining 29348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 39563 2.07 - 4.13: 589 4.13 - 6.20: 62 6.20 - 8.27: 17 8.27 - 10.33: 4 Bond angle restraints: 40235 Sorted by residual: angle pdb=" CA GLN H 370 " pdb=" CB GLN H 370 " pdb=" CG GLN H 370 " ideal model delta sigma weight residual 114.10 121.14 -7.04 2.00e+00 2.50e-01 1.24e+01 angle pdb=" C LEU D 122 " pdb=" N THR D 123 " pdb=" CA THR D 123 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.24e+01 angle pdb=" CB LYS D 80 " pdb=" CG LYS D 80 " pdb=" CD LYS D 80 " ideal model delta sigma weight residual 111.30 119.37 -8.07 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CB MET A 345 " pdb=" CG MET A 345 " pdb=" SD MET A 345 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB ARG D 312 " pdb=" CG ARG D 312 " pdb=" CD ARG D 312 " ideal model delta sigma weight residual 111.30 118.98 -7.68 2.30e+00 1.89e-01 1.12e+01 ... (remaining 40230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 16463 34.77 - 69.53: 1043 69.53 - 104.30: 88 104.30 - 139.07: 1 139.07 - 173.83: 4 Dihedral angle restraints: 17599 sinusoidal: 7953 harmonic: 9646 Sorted by residual: dihedral pdb=" O4' U C 32 " pdb=" C1' U C 32 " pdb=" N1 U C 32 " pdb=" C2 U C 32 " ideal model delta sinusoidal sigma weight residual 200.00 49.31 150.69 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual 200.00 53.19 146.81 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual -128.00 45.83 -173.83 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 17596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4134 0.081 - 0.161: 299 0.161 - 0.242: 7 0.242 - 0.322: 0 0.322 - 0.403: 1 Chirality restraints: 4441 Sorted by residual: chirality pdb=" CB ILE B 147 " pdb=" CA ILE B 147 " pdb=" CG1 ILE B 147 " pdb=" CG2 ILE B 147 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CB VAL G 357 " pdb=" CA VAL G 357 " pdb=" CG1 VAL G 357 " pdb=" CG2 VAL G 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" C3' C C 47 " pdb=" C4' C C 47 " pdb=" O3' C C 47 " pdb=" C2' C C 47 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 4438 not shown) Planarity restraints: 4837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 320 " 0.065 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO H 321 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO H 321 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 321 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 351 " 0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 352 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 391 " 0.017 2.00e-02 2.50e+03 1.75e-02 7.64e+00 pdb=" CG TRP J 391 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP J 391 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP J 391 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP J 391 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 391 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 391 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 391 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 391 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP J 391 " -0.002 2.00e-02 2.50e+03 ... (remaining 4834 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 138 2.47 - 3.08: 17781 3.08 - 3.69: 43143 3.69 - 4.29: 62277 4.29 - 4.90: 106199 Nonbonded interactions: 229538 Sorted by model distance: nonbonded pdb=" NH2 ARG A 287 " pdb=" OP1 DA T 10 " model vdw 1.865 3.120 nonbonded pdb=" OH TYR D 315 " pdb=" O PRO E 266 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 346 " pdb=" OD1 ASN A 348 " model vdw 2.236 3.040 nonbonded pdb=" O ALA D 247 " pdb=" OG1 THR D 251 " model vdw 2.239 3.040 nonbonded pdb=" O PHE H 90 " pdb=" OG1 THR H 97 " model vdw 2.241 3.040 ... (remaining 229533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 1 through 370) selection = (chain 'E' and (resid 1 through 189 or resid 210 through 370)) selection = (chain 'F' and (resid 1 through 189 or resid 210 through 370)) selection = (chain 'G' and (resid 1 through 189 or resid 210 through 370)) selection = (chain 'H' and (resid 1 through 189 or resid 210 through 370)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.090 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 0.043 29361 Z= 0.140 Angle : 0.619 10.335 40247 Z= 0.329 Chirality : 0.043 0.403 4441 Planarity : 0.005 0.097 4837 Dihedral : 20.617 173.832 11379 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.54 % Allowed : 34.33 % Favored : 65.13 % 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 aren not related in a simple way. whole: -0.99 (0.14), residues: 3305 helix: 0.02 (0.15), residues: 1153 sheet: 0.31 (0.22), residues: 533 loop : -1.50 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 345 TYR 0.017 0.001 TYR G 307 PHE 0.029 0.001 PHE G 244 TRP 0.048 0.001 TRP J 391 HIS 0.006 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00296 (29353) covalent geometry : angle 0.61733 (40235) hydrogen bonds : bond 0.16870 ( 1151) hydrogen bonds : angle 6.56014 ( 3266) metal coordination : bond 0.00296 ( 8) metal coordination : angle 2.51190 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7303 (t70) cc_final: 0.7081 (t70) outliers start: 15 outliers final: 5 residues processed: 307 average time/residue: 0.1800 time to fit residues: 88.3868 Evaluate side-chains 286 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 281 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 238 GLN B 61 GLN B 135 HIS D 11 HIS D 69 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN D 370 GLN E 11 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 HIS J 200 ASN J 302 HIS K 14 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100384 restraints weight = 52856.938| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.15 r_work: 0.3052 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 29361 Z= 0.275 Angle : 0.645 8.194 40247 Z= 0.343 Chirality : 0.044 0.232 4441 Planarity : 0.005 0.071 4837 Dihedral : 16.565 177.471 5050 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.03 % Allowed : 30.84 % Favored : 64.13 % 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 aren not related in a simple way. whole: -0.82 (0.14), residues: 3305 helix: 0.40 (0.15), residues: 1172 sheet: 0.17 (0.22), residues: 516 loop : -1.52 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 67 TYR 0.021 0.002 TYR E 265 PHE 0.030 0.002 PHE J 444 TRP 0.019 0.002 TRP H 78 HIS 0.008 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00626 (29353) covalent geometry : angle 0.64244 (40235) hydrogen bonds : bond 0.05279 ( 1151) hydrogen bonds : angle 4.97396 ( 3266) metal coordination : bond 0.00654 ( 8) metal coordination : angle 3.44655 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 279 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7657 (mtt-85) REVERT: D 78 TRP cc_start: 0.6345 (OUTLIER) cc_final: 0.4720 (t-100) REVERT: D 312 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7543 (tpm170) REVERT: F 69 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7172 (tp40) REVERT: F 370 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6905 (tp40) REVERT: G 62 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.7547 (mtp180) REVERT: I 209 MET cc_start: 0.8788 (mpp) cc_final: 0.8208 (mmm) REVERT: J 199 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6485 (m-70) outliers start: 141 outliers final: 66 residues processed: 396 average time/residue: 0.1803 time to fit residues: 115.4791 Evaluate side-chains 335 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 370 GLN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 199 HIS Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 47 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 331 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 330 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS F 9 GLN H 118 ASN J 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106150 restraints weight = 52738.897| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.05 r_work: 0.3111 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29361 Z= 0.113 Angle : 0.526 7.362 40247 Z= 0.277 Chirality : 0.040 0.189 4441 Planarity : 0.004 0.058 4837 Dihedral : 16.467 177.534 5045 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.25 % Allowed : 31.94 % Favored : 64.81 % 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 aren not related in a simple way. whole: -0.42 (0.15), residues: 3305 helix: 0.86 (0.15), residues: 1185 sheet: 0.36 (0.22), residues: 520 loop : -1.40 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 332 TYR 0.012 0.001 TYR E 218 PHE 0.013 0.001 PHE H 364 TRP 0.016 0.001 TRP J 391 HIS 0.006 0.001 HIS J 199 Details of bonding type rmsd covalent geometry : bond 0.00247 (29353) covalent geometry : angle 0.52466 (40235) hydrogen bonds : bond 0.03772 ( 1151) hydrogen bonds : angle 4.50469 ( 3266) metal coordination : bond 0.00273 ( 8) metal coordination : angle 2.41948 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 303 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.6437 (t80) cc_final: 0.6232 (t80) REVERT: B 162 ASP cc_start: 0.7768 (t70) cc_final: 0.7346 (t70) REVERT: D 46 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9063 (mp) REVERT: D 66 ASP cc_start: 0.7740 (m-30) cc_final: 0.7404 (t0) REVERT: D 78 TRP cc_start: 0.5900 (OUTLIER) cc_final: 0.4421 (t-100) REVERT: D 257 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7049 (tp40) REVERT: F 69 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7550 (tp40) REVERT: F 370 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: I 56 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5992 (pt) REVERT: I 209 MET cc_start: 0.8761 (mpp) cc_final: 0.8231 (mmm) REVERT: I 332 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7781 (ttt-90) REVERT: J 110 ASP cc_start: 0.7747 (t70) cc_final: 0.7413 (m-30) REVERT: J 199 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6520 (m-70) REVERT: J 247 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8257 (m-80) outliers start: 91 outliers final: 45 residues processed: 376 average time/residue: 0.1882 time to fit residues: 111.7825 Evaluate side-chains 327 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 370 GLN Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain J residue 199 HIS Chi-restraints excluded: chain J residue 247 PHE Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 chunk 262 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 201 ASN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS F 17 ASN I 235 ASN J 199 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100188 restraints weight = 52681.293| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.95 r_work: 0.3021 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 29361 Z= 0.315 Angle : 0.673 10.042 40247 Z= 0.356 Chirality : 0.045 0.194 4441 Planarity : 0.005 0.063 4837 Dihedral : 16.505 177.419 5045 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 5.46 % Allowed : 30.44 % Favored : 64.10 % 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 aren not related in a simple way. whole: -0.75 (0.15), residues: 3305 helix: 0.55 (0.15), residues: 1183 sheet: 0.02 (0.22), residues: 519 loop : -1.49 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 332 TYR 0.027 0.002 TYR E 218 PHE 0.020 0.002 PHE I 52 TRP 0.015 0.002 TRP H 366 HIS 0.007 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00724 (29353) covalent geometry : angle 0.66992 (40235) hydrogen bonds : bond 0.05229 ( 1151) hydrogen bonds : angle 4.84688 ( 3266) metal coordination : bond 0.00835 ( 8) metal coordination : angle 4.04466 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 271 time to evaluate : 0.965 Fit side-chains REVERT: A 151 LEU cc_start: 0.8980 (mp) cc_final: 0.8703 (mt) REVERT: A 310 HIS cc_start: 0.7224 (t70) cc_final: 0.6923 (t-90) REVERT: A 313 TYR cc_start: 0.6667 (t80) cc_final: 0.6464 (t80) REVERT: B 147 ILE cc_start: 0.5539 (OUTLIER) cc_final: 0.5259 (tp) REVERT: D 46 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9043 (mp) REVERT: D 78 TRP cc_start: 0.6052 (OUTLIER) cc_final: 0.4635 (t-100) REVERT: D 337 TYR cc_start: 0.6013 (t80) cc_final: 0.5789 (t80) REVERT: F 69 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7142 (tp40) REVERT: F 147 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8223 (ttp-170) REVERT: G 62 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.7829 (mtp180) REVERT: I 56 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6638 (pt) REVERT: I 332 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7845 (ttt-90) REVERT: J 199 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.6600 (m-70) outliers start: 153 outliers final: 90 residues processed: 396 average time/residue: 0.1754 time to fit residues: 111.3416 Evaluate side-chains 361 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 262 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 370 GLN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 138 CYS Chi-restraints excluded: chain J residue 199 HIS Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 15 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 90 optimal weight: 0.0470 chunk 174 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 332 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 201 ASN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN D 10 ASN D 69 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS F 17 ASN H 17 ASN H 118 ASN J 199 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104471 restraints weight = 52336.358| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.02 r_work: 0.3116 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29361 Z= 0.112 Angle : 0.532 7.789 40247 Z= 0.279 Chirality : 0.040 0.165 4441 Planarity : 0.004 0.053 4837 Dihedral : 16.448 177.794 5045 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.82 % Allowed : 31.76 % Favored : 64.42 % 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 aren not related in a simple way. whole: -0.32 (0.15), residues: 3305 helix: 1.02 (0.15), residues: 1190 sheet: 0.35 (0.22), residues: 510 loop : -1.38 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 49 TYR 0.015 0.001 TYR E 218 PHE 0.019 0.001 PHE G 244 TRP 0.018 0.001 TRP J 391 HIS 0.004 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00245 (29353) covalent geometry : angle 0.53025 (40235) hydrogen bonds : bond 0.03587 ( 1151) hydrogen bonds : angle 4.38607 ( 3266) metal coordination : bond 0.00304 ( 8) metal coordination : angle 2.65494 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 283 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7778 (t70) cc_final: 0.7358 (t70) REVERT: D 46 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9058 (mp) REVERT: D 78 TRP cc_start: 0.5782 (OUTLIER) cc_final: 0.4255 (t-100) REVERT: F 69 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7596 (tp40) REVERT: F 147 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7850 (ttp-170) REVERT: G 62 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: I 4 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: I 56 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6153 (pt) REVERT: I 209 MET cc_start: 0.8774 (mpp) cc_final: 0.8226 (mmm) REVERT: I 332 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7787 (ttt-90) REVERT: J 110 ASP cc_start: 0.7866 (t70) cc_final: 0.7503 (t70) REVERT: J 166 TYR cc_start: 0.7532 (m-80) cc_final: 0.7306 (m-80) REVERT: J 199 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6447 (m-70) REVERT: J 247 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: J 407 ASP cc_start: 0.8386 (p0) cc_final: 0.8163 (p0) REVERT: K 2 ASN cc_start: 0.5914 (p0) cc_final: 0.5689 (p0) REVERT: K 150 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8473 (mm-30) outliers start: 107 outliers final: 61 residues processed: 372 average time/residue: 0.1531 time to fit residues: 91.0978 Evaluate side-chains 340 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain J residue 199 HIS Chi-restraints excluded: chain J residue 247 PHE Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 53 optimal weight: 0.9990 chunk 134 optimal weight: 0.0070 chunk 64 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 0.2980 chunk 117 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 overall best weight: 3.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 201 ASN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN D 70 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN E 11 HIS H 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101900 restraints weight = 52515.856| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.95 r_work: 0.3041 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29361 Z= 0.225 Angle : 0.600 8.373 40247 Z= 0.316 Chirality : 0.043 0.177 4441 Planarity : 0.004 0.047 4837 Dihedral : 16.416 178.950 5045 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.68 % Allowed : 31.23 % Favored : 64.10 % 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 aren not related in a simple way. whole: -0.48 (0.15), residues: 3305 helix: 0.87 (0.15), residues: 1186 sheet: 0.14 (0.22), residues: 512 loop : -1.40 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 332 TYR 0.023 0.001 TYR E 218 PHE 0.016 0.002 PHE I 52 TRP 0.012 0.001 TRP H 366 HIS 0.006 0.001 HIS D 11 Details of bonding type rmsd covalent geometry : bond 0.00517 (29353) covalent geometry : angle 0.59743 (40235) hydrogen bonds : bond 0.04446 ( 1151) hydrogen bonds : angle 4.55322 ( 3266) metal coordination : bond 0.00621 ( 8) metal coordination : angle 3.36883 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 276 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7261 (t70) cc_final: 0.6993 (t-90) REVERT: D 46 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9041 (mp) REVERT: D 78 TRP cc_start: 0.5739 (OUTLIER) cc_final: 0.4253 (t-100) REVERT: D 154 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7640 (tmmt) REVERT: E 109 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7540 (ptmt) REVERT: F 69 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7366 (tp40) REVERT: F 147 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7954 (ttp-170) REVERT: G 62 ARG cc_start: 0.9395 (OUTLIER) cc_final: 0.7782 (mtp180) REVERT: H 62 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7012 (ttp-170) REVERT: I 4 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: I 56 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6485 (pt) REVERT: I 332 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7872 (ttt-90) REVERT: J 166 TYR cc_start: 0.7604 (m-80) cc_final: 0.7339 (m-80) REVERT: K 2 ASN cc_start: 0.6180 (p0) cc_final: 0.5688 (p0) outliers start: 131 outliers final: 86 residues processed: 382 average time/residue: 0.1694 time to fit residues: 103.4279 Evaluate side-chains 362 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 266 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 212 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 147 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 201 ASN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS F 229 ASN H 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102516 restraints weight = 52575.204| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.91 r_work: 0.3058 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29361 Z= 0.200 Angle : 0.586 8.127 40247 Z= 0.308 Chirality : 0.042 0.177 4441 Planarity : 0.004 0.050 4837 Dihedral : 16.394 178.764 5045 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.68 % Allowed : 31.08 % Favored : 64.24 % 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 aren not related in a simple way. whole: -0.49 (0.15), residues: 3305 helix: 0.87 (0.15), residues: 1189 sheet: 0.11 (0.22), residues: 514 loop : -1.41 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 312 TYR 0.020 0.001 TYR E 218 PHE 0.015 0.001 PHE I 244 TRP 0.015 0.001 TRP F 366 HIS 0.004 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00461 (29353) covalent geometry : angle 0.58359 (40235) hydrogen bonds : bond 0.04257 ( 1151) hydrogen bonds : angle 4.52727 ( 3266) metal coordination : bond 0.00540 ( 8) metal coordination : angle 3.28016 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 276 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7270 (t70) cc_final: 0.6960 (t-90) REVERT: B 147 ILE cc_start: 0.5405 (OUTLIER) cc_final: 0.5163 (tp) REVERT: B 162 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7381 (t70) REVERT: D 46 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9039 (mp) REVERT: D 70 GLN cc_start: 0.8393 (mp-120) cc_final: 0.8153 (mp10) REVERT: D 78 TRP cc_start: 0.5671 (OUTLIER) cc_final: 0.4159 (t-100) REVERT: D 154 LYS cc_start: 0.7846 (tmmt) cc_final: 0.7637 (tmmt) REVERT: D 210 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5566 (m-80) REVERT: E 109 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7590 (ptmt) REVERT: F 69 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7345 (tp40) REVERT: F 147 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7936 (ttp-170) REVERT: G 62 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.7765 (mtp180) REVERT: H 62 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.6992 (ttp-170) REVERT: I 4 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: I 56 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6322 (pt) REVERT: I 332 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7966 (ttt-90) REVERT: J 110 ASP cc_start: 0.8025 (t70) cc_final: 0.7540 (t70) REVERT: J 166 TYR cc_start: 0.7601 (m-80) cc_final: 0.7343 (m-80) REVERT: K 2 ASN cc_start: 0.6174 (p0) cc_final: 0.5672 (p0) outliers start: 131 outliers final: 88 residues processed: 382 average time/residue: 0.1619 time to fit residues: 99.8127 Evaluate side-chains 371 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 270 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 346 ASN Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 212 ASP Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 194 optimal weight: 3.9990 chunk 265 optimal weight: 0.0980 chunk 262 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 293 optimal weight: 0.0000 chunk 233 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 129 optimal weight: 0.0270 chunk 43 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 overall best weight: 0.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN D 10 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN E 10 ASN ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106791 restraints weight = 52384.976| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.01 r_work: 0.3146 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 29361 Z= 0.105 Angle : 0.527 8.109 40247 Z= 0.274 Chirality : 0.040 0.179 4441 Planarity : 0.004 0.057 4837 Dihedral : 16.338 179.770 5045 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.18 % Allowed : 32.37 % Favored : 64.45 % 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 aren not related in a simple way. whole: -0.11 (0.15), residues: 3305 helix: 1.20 (0.16), residues: 1196 sheet: 0.50 (0.22), residues: 521 loop : -1.30 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 332 TYR 0.015 0.001 TYR H 316 PHE 0.020 0.001 PHE G 244 TRP 0.021 0.001 TRP J 391 HIS 0.006 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00223 (29353) covalent geometry : angle 0.52561 (40235) hydrogen bonds : bond 0.03205 ( 1151) hydrogen bonds : angle 4.19489 ( 3266) metal coordination : bond 0.00264 ( 8) metal coordination : angle 2.41186 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 300 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7193 (mtm180) cc_final: 0.6984 (mtm-85) REVERT: B 162 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7273 (t70) REVERT: B 232 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8147 (pt) REVERT: D 46 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9051 (mp) REVERT: D 103 MET cc_start: 0.8211 (ttp) cc_final: 0.7976 (tmm) REVERT: D 154 LYS cc_start: 0.7864 (tmmt) cc_final: 0.7647 (tmmt) REVERT: D 359 ASP cc_start: 0.7721 (p0) cc_final: 0.7019 (t0) REVERT: E 109 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7706 (ptmt) REVERT: F 69 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7649 (tp-100) REVERT: F 147 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7755 (ttp-170) REVERT: G 62 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.7863 (mtp180) REVERT: I 4 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: I 56 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6049 (pt) REVERT: I 209 MET cc_start: 0.8784 (mpp) cc_final: 0.8300 (mmm) REVERT: I 332 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7972 (ttt-90) REVERT: J 110 ASP cc_start: 0.7975 (t70) cc_final: 0.7414 (t70) REVERT: J 166 TYR cc_start: 0.7481 (m-80) cc_final: 0.7272 (m-80) REVERT: J 247 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: K 2 ASN cc_start: 0.5941 (p0) cc_final: 0.5593 (p0) REVERT: K 150 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8407 (mm-30) outliers start: 89 outliers final: 56 residues processed: 375 average time/residue: 0.1646 time to fit residues: 97.6693 Evaluate side-chains 348 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 280 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 247 PHE Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 50 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 266 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 chunk 102 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 272 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104309 restraints weight = 52411.403| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.11 r_work: 0.3106 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29361 Z= 0.138 Angle : 0.546 7.568 40247 Z= 0.284 Chirality : 0.040 0.160 4441 Planarity : 0.004 0.064 4837 Dihedral : 16.242 179.118 5045 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.86 % Allowed : 32.76 % Favored : 64.38 % 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 aren not related in a simple way. whole: -0.07 (0.15), residues: 3305 helix: 1.24 (0.16), residues: 1196 sheet: 0.53 (0.22), residues: 516 loop : -1.28 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 49 TYR 0.016 0.001 TYR E 218 PHE 0.016 0.001 PHE G 244 TRP 0.025 0.001 TRP F 366 HIS 0.004 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00316 (29353) covalent geometry : angle 0.54380 (40235) hydrogen bonds : bond 0.03587 ( 1151) hydrogen bonds : angle 4.23265 ( 3266) metal coordination : bond 0.00347 ( 8) metal coordination : angle 2.63101 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7342 (t70) REVERT: B 232 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8203 (pt) REVERT: D 46 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9058 (mp) REVERT: D 154 LYS cc_start: 0.7863 (tmmt) cc_final: 0.7639 (tmmt) REVERT: E 109 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7809 (ptmt) REVERT: E 218 TYR cc_start: 0.8364 (t80) cc_final: 0.8039 (t80) REVERT: F 69 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: F 147 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7758 (ttp-170) REVERT: G 62 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: I 4 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: I 56 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6107 (pt) REVERT: I 332 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7838 (ttt-90) REVERT: J 110 ASP cc_start: 0.7986 (t70) cc_final: 0.7569 (t70) REVERT: J 166 TYR cc_start: 0.7567 (m-80) cc_final: 0.7349 (m-80) REVERT: K 2 ASN cc_start: 0.5983 (p0) cc_final: 0.5668 (p0) outliers start: 80 outliers final: 59 residues processed: 351 average time/residue: 0.1603 time to fit residues: 89.6267 Evaluate side-chains 347 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 278 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 40 GLN Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 170 PHE Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 205 optimal weight: 0.9990 chunk 214 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 276 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS E 17 ASN F 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103470 restraints weight = 52248.697| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.96 r_work: 0.3088 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29361 Z= 0.158 Angle : 0.561 8.420 40247 Z= 0.293 Chirality : 0.041 0.167 4441 Planarity : 0.004 0.058 4837 Dihedral : 16.197 179.499 5045 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.10 % Allowed : 32.51 % Favored : 64.38 % 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 aren not related in a simple way. whole: -0.13 (0.15), residues: 3305 helix: 1.18 (0.15), residues: 1192 sheet: 0.44 (0.22), residues: 516 loop : -1.28 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 49 TYR 0.018 0.001 TYR E 218 PHE 0.014 0.001 PHE I 244 TRP 0.026 0.001 TRP F 366 HIS 0.004 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00365 (29353) covalent geometry : angle 0.55900 (40235) hydrogen bonds : bond 0.03826 ( 1151) hydrogen bonds : angle 4.31368 ( 3266) metal coordination : bond 0.00418 ( 8) metal coordination : angle 2.95129 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 310 HIS cc_start: 0.7221 (t70) cc_final: 0.6946 (t-90) REVERT: B 162 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7348 (t70) REVERT: B 232 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8231 (pt) REVERT: D 46 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9047 (mp) REVERT: D 70 GLN cc_start: 0.8418 (mp-120) cc_final: 0.8079 (mp10) REVERT: D 103 MET cc_start: 0.8223 (ttp) cc_final: 0.7973 (tmm) REVERT: E 109 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7810 (ptmt) REVERT: E 218 TYR cc_start: 0.8350 (t80) cc_final: 0.8011 (t80) REVERT: F 69 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7428 (tp40) REVERT: F 147 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7867 (ttp-170) REVERT: G 62 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.7661 (mtp180) REVERT: H 148 MET cc_start: 0.8711 (tmm) cc_final: 0.8419 (ppp) REVERT: H 293 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: I 4 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: I 56 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6183 (pt) REVERT: I 332 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7893 (ttt-90) REVERT: I 352 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8048 (mm-30) REVERT: J 110 ASP cc_start: 0.8047 (t70) cc_final: 0.7653 (t70) REVERT: J 166 TYR cc_start: 0.7556 (m-80) cc_final: 0.7345 (m-80) REVERT: K 2 ASN cc_start: 0.6080 (p0) cc_final: 0.5762 (p0) REVERT: K 22 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8935 (tp) outliers start: 87 outliers final: 61 residues processed: 354 average time/residue: 0.1765 time to fit residues: 99.4829 Evaluate side-chains 349 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 346 ASN Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 322 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 267 TRP Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 214 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 338 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN F 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103835 restraints weight = 52479.561| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.97 r_work: 0.3098 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29361 Z= 0.138 Angle : 0.556 9.493 40247 Z= 0.290 Chirality : 0.040 0.162 4441 Planarity : 0.004 0.056 4837 Dihedral : 16.195 179.593 5045 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.89 % Allowed : 32.91 % Favored : 64.20 % 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 aren not related in a simple way. whole: -0.14 (0.15), residues: 3305 helix: 1.17 (0.15), residues: 1197 sheet: 0.48 (0.22), residues: 512 loop : -1.30 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 49 TYR 0.016 0.001 TYR E 218 PHE 0.017 0.001 PHE G 244 TRP 0.032 0.001 TRP J 391 HIS 0.003 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00317 (29353) covalent geometry : angle 0.55393 (40235) hydrogen bonds : bond 0.03719 ( 1151) hydrogen bonds : angle 4.28281 ( 3266) metal coordination : bond 0.00369 ( 8) metal coordination : angle 2.88986 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6850.72 seconds wall clock time: 117 minutes 56.89 seconds (7076.89 seconds total)