Starting phenix.real_space_refine on Tue Jun 24 04:28:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yha_39286/06_2025/8yha_39286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yha_39286/06_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_39286/06_2025/8yha_39286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yha_39286/06_2025/8yha_39286.map" model { file = "/net/cci-nas-00/data/ceres_data/8yha_39286/06_2025/8yha_39286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yha_39286/06_2025/8yha_39286.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.94, per 1000 atoms: 0.63 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: 8.11 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 9.29 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: 10.82 Time building geometry restraints manager: 9.61 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: 19.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.230 Set scattering table: 0.320 Process input model: 79.400 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.140 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.730 ------------------------------------------------------------------------------- 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 : 6.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.048 0.001 TRP J 391 HIS 0.006 0.001 HIS G 204 PHE 0.029 0.001 PHE G 244 TYR 0.017 0.001 TYR G 307 ARG 0.011 0.000 ARG F 345 Details of bonding type rmsd hydrogen bonds : bond 0.16870 ( 1151) hydrogen bonds : angle 6.56014 ( 3266) metal coordination : bond 0.00296 ( 8) metal coordination : angle 2.51190 ( 12) covalent geometry : bond 0.00296 (29353) covalent geometry : angle 0.61733 (40235) *********************** 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 : 3.266 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: 0.4535 time to fit residues: 222.7650 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 : 3.298 ------------------------------------------------------------------------------- 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 286 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 307 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 238 GLN B 61 GLN B 135 HIS ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100082 restraints weight = 52534.247| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.14 r_work: 0.3045 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 29361 Z= 0.290 Angle : 0.663 8.745 40247 Z= 0.352 Chirality : 0.045 0.231 4441 Planarity : 0.005 0.069 4837 Dihedral : 16.576 176.991 5050 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.10 % Allowed : 30.94 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3305 helix: 0.36 (0.15), residues: 1173 sheet: 0.13 (0.22), residues: 504 loop : -1.52 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 78 HIS 0.008 0.001 HIS G 180 PHE 0.032 0.002 PHE J 444 TYR 0.023 0.002 TYR E 265 ARG 0.005 0.001 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 1151) hydrogen bonds : angle 4.97665 ( 3266) metal coordination : bond 0.00719 ( 8) metal coordination : angle 3.65166 ( 12) covalent geometry : bond 0.00665 (29353) covalent geometry : angle 0.66023 (40235) *********************** 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: 143 poor density : 277 time to evaluate : 3.224 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.9015 (mp) cc_final: 0.8732 (mt) REVERT: B 79 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7646 (mtt-85) REVERT: D 78 TRP cc_start: 0.6398 (OUTLIER) cc_final: 0.4770 (t-100) REVERT: F 69 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7081 (tp40) REVERT: F 370 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6926 (tp40) REVERT: G 62 ARG cc_start: 0.9384 (OUTLIER) cc_final: 0.7555 (mtp180) REVERT: J 199 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6527 (m-70) outliers start: 143 outliers final: 68 residues processed: 398 average time/residue: 0.3872 time to fit residues: 249.1085 Evaluate side-chains 335 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 261 time to evaluate : 3.084 ------------------------------------------------------------------------------- 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 296 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 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 97 THR Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 105 LYS 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 361 ILE Chi-restraints excluded: chain H residue 364 PHE Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 245 LEU 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 138 CYS 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 J residue 440 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 12 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 303 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.129844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105055 restraints weight = 52434.047| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.94 r_work: 0.3106 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29361 Z= 0.129 Angle : 0.538 7.228 40247 Z= 0.284 Chirality : 0.040 0.191 4441 Planarity : 0.004 0.058 4837 Dihedral : 16.477 176.952 5045 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.57 % Allowed : 32.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3305 helix: 0.83 (0.15), residues: 1176 sheet: 0.31 (0.22), residues: 506 loop : -1.39 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 391 HIS 0.004 0.001 HIS J 199 PHE 0.013 0.001 PHE H 364 TYR 0.010 0.001 TYR I 360 ARG 0.004 0.000 ARG G 332 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 1151) hydrogen bonds : angle 4.56077 ( 3266) metal coordination : bond 0.00325 ( 8) metal coordination : angle 2.66344 ( 12) covalent geometry : bond 0.00285 (29353) covalent geometry : angle 0.53635 (40235) *********************** 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 397 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 297 time to evaluate : 3.088 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7746 (t70) cc_final: 0.7343 (t70) REVERT: D 46 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9054 (mp) REVERT: D 78 TRP cc_start: 0.5980 (OUTLIER) cc_final: 0.4464 (t-100) REVERT: D 257 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7043 (tp40) REVERT: F 69 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7450 (tp40) REVERT: F 370 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6766 (tp40) REVERT: I 56 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6040 (pt) REVERT: I 209 MET cc_start: 0.8774 (mpp) cc_final: 0.8239 (mmm) REVERT: I 332 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7759 (ttt-90) REVERT: J 110 ASP cc_start: 0.7713 (t70) cc_final: 0.7348 (m-30) REVERT: J 199 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6625 (m-70) REVERT: J 247 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8262 (m-80) outliers start: 100 outliers final: 53 residues processed: 379 average time/residue: 0.4665 time to fit residues: 279.8866 Evaluate side-chains 333 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 3.582 ------------------------------------------------------------------------------- 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 83 ILE 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 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 104 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 370 GLN Chi-restraints excluded: chain G residue 3 ILE 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 166 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 181 ILE 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 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 231 THR 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 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 95 optimal weight: 0.0060 chunk 300 optimal weight: 4.9990 chunk 241 optimal weight: 0.0470 chunk 275 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 182 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 overall best weight: 0.4694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN E 10 ASN E 11 HIS F 17 ASN H 17 ASN H 86 ASN J 199 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107120 restraints weight = 52885.411| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.00 r_work: 0.3138 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29361 Z= 0.098 Angle : 0.508 7.403 40247 Z= 0.266 Chirality : 0.039 0.170 4441 Planarity : 0.004 0.066 4837 Dihedral : 16.413 178.937 5045 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.39 % Allowed : 32.05 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3305 helix: 1.11 (0.16), residues: 1190 sheet: 0.49 (0.22), residues: 510 loop : -1.36 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 391 HIS 0.004 0.001 HIS J 199 PHE 0.016 0.001 PHE K 146 TYR 0.013 0.001 TYR I 360 ARG 0.008 0.000 ARG K 49 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 1151) hydrogen bonds : angle 4.30960 ( 3266) metal coordination : bond 0.00249 ( 8) metal coordination : angle 2.25391 ( 12) covalent geometry : bond 0.00210 (29353) covalent geometry : angle 0.50622 (40235) *********************** 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 405 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 310 time to evaluate : 7.116 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7830 (t70) cc_final: 0.7350 (t70) REVERT: D 46 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9044 (mp) REVERT: D 78 TRP cc_start: 0.5627 (OUTLIER) cc_final: 0.4954 (t-100) REVERT: D 257 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7122 (tp40) REVERT: D 359 ASP cc_start: 0.7775 (p0) cc_final: 0.7037 (t0) REVERT: F 69 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7643 (tp40) REVERT: F 147 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7776 (ttp-170) REVERT: H 148 MET cc_start: 0.8639 (tmm) cc_final: 0.8338 (ppp) REVERT: I 4 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: I 56 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.6016 (pt) REVERT: I 168 GLU cc_start: 0.8621 (mp0) cc_final: 0.8283 (mp0) REVERT: I 209 MET cc_start: 0.8786 (mpp) cc_final: 0.8284 (mmm) REVERT: I 332 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7817 (ttt-90) REVERT: J 110 ASP cc_start: 0.7847 (t70) cc_final: 0.7306 (m-30) REVERT: J 199 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6609 (m-70) REVERT: J 247 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: K 2 ASN cc_start: 0.5762 (p0) cc_final: 0.5521 (p0) REVERT: K 150 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8437 (mm-30) outliers start: 95 outliers final: 53 residues processed: 388 average time/residue: 0.6273 time to fit residues: 397.0906 Evaluate side-chains 344 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 280 time to evaluate : 3.567 ------------------------------------------------------------------------------- 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 207 ILE 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 69 VAL 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 186 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 257 GLN 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 75 THR 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 166 THR 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 116 LEU Chi-restraints excluded: chain H residue 190 VAL 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 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 I residue 353 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 285 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS A 201 ASN A 310 HIS 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 I 204 HIS I 235 ASN J 199 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.098257 restraints weight = 52657.258| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.11 r_work: 0.3007 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 29361 Z= 0.402 Angle : 0.750 11.423 40247 Z= 0.395 Chirality : 0.048 0.203 4441 Planarity : 0.005 0.067 4837 Dihedral : 16.496 178.290 5045 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 6.25 % Allowed : 29.59 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3305 helix: 0.45 (0.15), residues: 1184 sheet: -0.10 (0.21), residues: 524 loop : -1.54 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 326 HIS 0.008 0.002 HIS G 180 PHE 0.023 0.002 PHE I 52 TYR 0.019 0.002 TYR E 265 ARG 0.010 0.001 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 1151) hydrogen bonds : angle 4.94970 ( 3266) metal coordination : bond 0.01111 ( 8) metal coordination : angle 4.54346 ( 12) covalent geometry : bond 0.00933 (29353) covalent geometry : angle 0.74574 (40235) *********************** 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 439 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 264 time to evaluate : 3.217 Fit side-chains REVERT: A 151 LEU cc_start: 0.8968 (mp) cc_final: 0.8711 (mt) REVERT: A 310 HIS cc_start: 0.7159 (t-90) cc_final: 0.6866 (t-90) REVERT: A 313 TYR cc_start: 0.6721 (t80) cc_final: 0.6520 (t80) REVERT: B 147 ILE cc_start: 0.5350 (OUTLIER) cc_final: 0.5115 (tp) REVERT: D 46 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9046 (mp) REVERT: D 154 LYS cc_start: 0.7837 (tmmt) cc_final: 0.7619 (tmmt) REVERT: D 267 ASP cc_start: 0.8457 (t0) cc_final: 0.8255 (t0) REVERT: E 109 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7498 (ptmt) REVERT: F 69 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7119 (tp40) REVERT: G 62 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.7686 (mtp180) REVERT: I 56 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6589 (pt) REVERT: I 332 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7970 (ttt-90) REVERT: J 166 TYR cc_start: 0.7727 (m-80) cc_final: 0.7453 (m-80) REVERT: J 199 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6608 (m-70) REVERT: K 2 ASN cc_start: 0.6152 (p0) cc_final: 0.5635 (p0) outliers start: 175 outliers final: 106 residues processed: 408 average time/residue: 0.3959 time to fit residues: 262.4897 Evaluate side-chains 371 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 257 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU 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 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 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 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 69 GLN 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 166 THR 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 245 LEU 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 79 LYS Chi-restraints excluded: chain E residue 109 LYS 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 86 ASN 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 230 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 340 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 117 ASP Chi-restraints excluded: chain G residue 122 LEU 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 G residue 313 LEU Chi-restraints excluded: chain G residue 346 ASN 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 167 VAL Chi-restraints excluded: chain I residue 179 THR 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 I residue 353 LEU 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 295 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 391 TRP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 212 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 259 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 276 optimal weight: 0.8980 chunk 319 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 B 193 GLN D 69 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS F 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.103431 restraints weight = 52535.143| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.96 r_work: 0.3092 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29361 Z= 0.127 Angle : 0.552 7.722 40247 Z= 0.291 Chirality : 0.040 0.170 4441 Planarity : 0.004 0.051 4837 Dihedral : 16.424 177.694 5045 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.43 % Allowed : 32.58 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3305 helix: 0.94 (0.15), residues: 1190 sheet: 0.23 (0.22), residues: 506 loop : -1.40 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 391 HIS 0.007 0.001 HIS J 199 PHE 0.014 0.001 PHE I 244 TYR 0.014 0.001 TYR B 29 ARG 0.007 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 1151) hydrogen bonds : angle 4.45751 ( 3266) metal coordination : bond 0.00344 ( 8) metal coordination : angle 2.99766 ( 12) covalent geometry : bond 0.00285 (29353) covalent geometry : angle 0.54990 (40235) *********************** 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 382 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 286 time to evaluate : 2.936 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7736 (t70) cc_final: 0.7300 (t70) REVERT: D 46 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9071 (mp) REVERT: D 78 TRP cc_start: 0.5791 (OUTLIER) cc_final: 0.4325 (t-100) REVERT: D 154 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7646 (tmmt) REVERT: D 267 ASP cc_start: 0.8505 (t0) cc_final: 0.8250 (t0) REVERT: E 141 ASP cc_start: 0.7875 (t0) cc_final: 0.7659 (t0) REVERT: F 69 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7306 (tp40) REVERT: F 147 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7936 (ttp-170) REVERT: H 62 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6961 (ttp-170) REVERT: H 148 MET cc_start: 0.8682 (tmm) cc_final: 0.8373 (ppp) REVERT: I 4 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: I 56 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6139 (pt) REVERT: I 332 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7912 (ttt-90) REVERT: J 166 TYR cc_start: 0.7610 (m-80) cc_final: 0.7355 (m-80) outliers start: 96 outliers final: 66 residues processed: 364 average time/residue: 0.4022 time to fit residues: 235.9037 Evaluate side-chains 344 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 270 time to evaluate : 3.142 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 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 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 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 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 75 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 108 ILE 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 F residue 358 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 171 LEU 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 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 167 VAL 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 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 440 LEU Chi-restraints excluded: chain J residue 447 SER 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 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 55 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 B 193 GLN 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100437 restraints weight = 52400.948| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.01 r_work: 0.3033 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29361 Z= 0.260 Angle : 0.635 9.720 40247 Z= 0.334 Chirality : 0.044 0.188 4441 Planarity : 0.004 0.047 4837 Dihedral : 16.388 178.834 5045 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.64 % Allowed : 31.66 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3305 helix: 0.74 (0.15), residues: 1186 sheet: -0.03 (0.22), residues: 514 loop : -1.46 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 366 HIS 0.006 0.001 HIS G 180 PHE 0.018 0.002 PHE I 52 TYR 0.019 0.002 TYR I 360 ARG 0.009 0.001 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 1151) hydrogen bonds : angle 4.65948 ( 3266) metal coordination : bond 0.00729 ( 8) metal coordination : angle 3.83628 ( 12) covalent geometry : bond 0.00600 (29353) covalent geometry : angle 0.63192 (40235) *********************** 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 404 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 274 time to evaluate : 3.221 Fit side-chains REVERT: B 162 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7372 (t70) REVERT: D 46 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9068 (mp) REVERT: D 78 TRP cc_start: 0.5904 (OUTLIER) cc_final: 0.4466 (t-100) REVERT: D 154 LYS cc_start: 0.7848 (tmmt) cc_final: 0.7639 (tmmt) REVERT: D 210 PHE cc_start: 0.5828 (OUTLIER) cc_final: 0.5358 (t80) REVERT: D 267 ASP cc_start: 0.8509 (t0) cc_final: 0.8298 (t0) REVERT: E 109 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7574 (ptmt) REVERT: F 69 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7320 (tp40) REVERT: G 62 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: H 62 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7009 (ttp-170) REVERT: I 4 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: I 56 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6495 (pt) REVERT: I 332 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7982 (ttt-90) REVERT: J 166 TYR cc_start: 0.7661 (m-80) cc_final: 0.7372 (m-80) REVERT: K 2 ASN cc_start: 0.6078 (p0) cc_final: 0.5655 (p0) outliers start: 130 outliers final: 82 residues processed: 379 average time/residue: 0.3988 time to fit residues: 244.7932 Evaluate side-chains 361 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 268 time to evaluate : 3.301 ------------------------------------------------------------------------------- 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 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 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 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 69 GLN 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 189 PHE Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 245 LEU 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 75 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 109 LYS 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 86 ASN 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 190 VAL 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 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 108 LEU 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 286 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 5 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS B 193 GLN D 69 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103212 restraints weight = 52620.032| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.98 r_work: 0.3093 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29361 Z= 0.139 Angle : 0.557 7.744 40247 Z= 0.292 Chirality : 0.041 0.169 4441 Planarity : 0.004 0.053 4837 Dihedral : 16.310 178.786 5045 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.00 % Allowed : 32.23 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3305 helix: 1.00 (0.15), residues: 1189 sheet: 0.22 (0.22), residues: 502 loop : -1.39 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 366 HIS 0.003 0.001 HIS B 220 PHE 0.017 0.001 PHE G 244 TYR 0.016 0.001 TYR I 360 ARG 0.007 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1151) hydrogen bonds : angle 4.38857 ( 3266) metal coordination : bond 0.00370 ( 8) metal coordination : angle 2.96678 ( 12) covalent geometry : bond 0.00315 (29353) covalent geometry : angle 0.55453 (40235) *********************** 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 397 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 285 time to evaluate : 3.086 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7320 (t70) REVERT: B 232 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8249 (pt) REVERT: D 46 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9065 (mp) REVERT: D 78 TRP cc_start: 0.5675 (OUTLIER) cc_final: 0.4186 (t-100) REVERT: D 154 LYS cc_start: 0.7853 (tmmt) cc_final: 0.7632 (tmmt) REVERT: D 185 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: D 210 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5545 (m-80) REVERT: D 267 ASP cc_start: 0.8499 (t0) cc_final: 0.8298 (t0) REVERT: E 109 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7652 (ptmt) REVERT: F 69 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7462 (tp40) REVERT: F 147 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7996 (ttp-170) REVERT: H 62 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6977 (ttp-170) REVERT: H 148 MET cc_start: 0.8675 (tmm) cc_final: 0.8390 (ppp) REVERT: H 293 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: I 4 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: I 56 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6152 (pt) REVERT: I 332 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7949 (ttt-90) REVERT: J 166 TYR cc_start: 0.7624 (m-80) cc_final: 0.7315 (m-80) REVERT: K 2 ASN cc_start: 0.6068 (p0) cc_final: 0.5853 (p0) outliers start: 112 outliers final: 79 residues processed: 377 average time/residue: 0.4037 time to fit residues: 246.3929 Evaluate side-chains 366 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 273 time to evaluate : 3.073 ------------------------------------------------------------------------------- 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 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 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 78 TRP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 185 GLU 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 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 79 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 322 VAL 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 100 LEU Chi-restraints excluded: chain F residue 101 VAL 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 340 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 3 ILE 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 G residue 171 LEU 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 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 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 167 VAL Chi-restraints excluded: chain I residue 190 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 96 SER 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 299 VAL Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain J residue 447 SER 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 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 251 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 281 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 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** F 17 ASN F 229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.102051 restraints weight = 52492.339| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.08 r_work: 0.3075 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29361 Z= 0.179 Angle : 0.579 8.290 40247 Z= 0.304 Chirality : 0.042 0.175 4441 Planarity : 0.004 0.049 4837 Dihedral : 16.263 179.662 5045 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.25 % Allowed : 32.01 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3305 helix: 0.95 (0.15), residues: 1191 sheet: 0.20 (0.22), residues: 504 loop : -1.38 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 391 HIS 0.004 0.001 HIS G 180 PHE 0.016 0.001 PHE G 244 TYR 0.016 0.001 TYR I 360 ARG 0.008 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 1151) hydrogen bonds : angle 4.43313 ( 3266) metal coordination : bond 0.00482 ( 8) metal coordination : angle 3.19598 ( 12) covalent geometry : bond 0.00411 (29353) covalent geometry : angle 0.57624 (40235) *********************** 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 391 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 272 time to evaluate : 3.138 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7388 (t70) REVERT: B 232 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8281 (pt) REVERT: D 46 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9059 (mp) REVERT: D 78 TRP cc_start: 0.5517 (OUTLIER) cc_final: 0.4079 (t-100) REVERT: D 154 LYS cc_start: 0.7866 (tmmt) cc_final: 0.7638 (tmmt) REVERT: D 185 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: D 210 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5536 (m-80) REVERT: E 109 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7730 (ptmt) REVERT: F 69 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7473 (tp40) REVERT: F 147 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8284 (ttp-170) REVERT: H 62 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7033 (ttp-170) REVERT: H 148 MET cc_start: 0.8687 (tmm) cc_final: 0.8394 (ppp) REVERT: I 4 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: I 56 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6293 (pt) REVERT: I 332 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7968 (ttt-90) REVERT: J 166 TYR cc_start: 0.7683 (m-80) cc_final: 0.7375 (m-80) REVERT: K 2 ASN cc_start: 0.6129 (p0) cc_final: 0.5899 (p0) outliers start: 119 outliers final: 93 residues processed: 371 average time/residue: 0.3903 time to fit residues: 234.4623 Evaluate side-chains 374 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 268 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU 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 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 41 SER 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 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 160 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 186 ILE 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 278 ILE 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 79 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 17 ASN 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 100 LEU Chi-restraints excluded: chain F residue 101 VAL 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 340 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 3 ILE 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 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 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 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 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 122 MET 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 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 353 GLN Chi-restraints excluded: chain J residue 440 LEU Chi-restraints excluded: chain J residue 447 SER 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 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 28 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 163 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 222 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 300 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104461 restraints weight = 52267.705| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.03 r_work: 0.3105 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29361 Z= 0.120 Angle : 0.545 10.387 40247 Z= 0.285 Chirality : 0.040 0.165 4441 Planarity : 0.004 0.053 4837 Dihedral : 16.246 179.739 5045 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.39 % Allowed : 32.83 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3305 helix: 1.09 (0.15), residues: 1195 sheet: 0.43 (0.22), residues: 505 loop : -1.34 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 391 HIS 0.004 0.001 HIS G 204 PHE 0.018 0.001 PHE G 244 TYR 0.014 0.001 TYR I 360 ARG 0.008 0.000 ARG D 332 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 1151) hydrogen bonds : angle 4.28883 ( 3266) metal coordination : bond 0.00301 ( 8) metal coordination : angle 2.77146 ( 12) covalent geometry : bond 0.00269 (29353) covalent geometry : angle 0.54302 (40235) ********************** 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 376 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 281 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7356 (t70) REVERT: D 46 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9054 (mp) REVERT: D 78 TRP cc_start: 0.5433 (OUTLIER) cc_final: 0.4062 (t-100) REVERT: D 103 MET cc_start: 0.8208 (ttp) cc_final: 0.7960 (ttp) REVERT: D 185 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: D 210 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: E 109 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7701 (ptmt) REVERT: F 69 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7444 (tp40) REVERT: F 147 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8026 (ttp-170) REVERT: F 312 ARG cc_start: 0.8378 (tmm-80) cc_final: 0.8107 (mtt-85) REVERT: H 148 MET cc_start: 0.8678 (tmm) cc_final: 0.8384 (ppp) REVERT: H 293 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: I 4 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: I 56 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6253 (pt) REVERT: I 209 MET cc_start: 0.8787 (mpp) cc_final: 0.8249 (mmm) REVERT: I 332 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7967 (ttt-90) REVERT: J 166 TYR cc_start: 0.7557 (m-80) cc_final: 0.7321 (m-80) REVERT: J 247 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: K 2 ASN cc_start: 0.6111 (p0) cc_final: 0.5869 (p0) REVERT: K 155 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8189 (mm-30) outliers start: 95 outliers final: 74 residues processed: 359 average time/residue: 0.4001 time to fit residues: 230.1106 Evaluate side-chains 357 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 270 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU 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 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 41 SER 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 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 160 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 210 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 75 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 305 SER 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 100 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain G residue 3 ILE 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 166 THR Chi-restraints excluded: chain G residue 171 LEU 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 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 167 VAL Chi-restraints excluded: chain I residue 190 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 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 247 PHE 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 J residue 447 SER 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 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 254 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 chunk 317 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS B 98 ASN B 193 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 17 ASN F 17 ASN H 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099442 restraints weight = 52557.739| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.06 r_work: 0.3028 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 29361 Z= 0.300 Angle : 0.681 10.790 40247 Z= 0.357 Chirality : 0.045 0.199 4441 Planarity : 0.005 0.057 4837 Dihedral : 16.289 179.769 5045 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.43 % Allowed : 31.87 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3305 helix: 0.67 (0.15), residues: 1187 sheet: -0.08 (0.21), residues: 524 loop : -1.47 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 366 HIS 0.006 0.001 HIS G 180 PHE 0.018 0.002 PHE I 52 TYR 0.018 0.002 TYR I 360 ARG 0.013 0.001 ARG K 49 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 1151) hydrogen bonds : angle 4.72623 ( 3266) metal coordination : bond 0.00835 ( 8) metal coordination : angle 4.28979 ( 12) covalent geometry : bond 0.00695 (29353) covalent geometry : angle 0.67719 (40235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16643.77 seconds wall clock time: 289 minutes 33.94 seconds (17373.94 seconds total)