Starting phenix.real_space_refine on Fri Jun 20 05:53:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3a_25652/06_2025/7t3a_25652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3a_25652/06_2025/7t3a_25652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3a_25652/06_2025/7t3a_25652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3a_25652/06_2025/7t3a_25652.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3a_25652/06_2025/7t3a_25652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3a_25652/06_2025/7t3a_25652.cif" } resolution = 4.0 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 131 5.16 5 C 14912 2.51 5 N 3942 2.21 5 O 4322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23310 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8120 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 41, 'TRANS': 948} Chain breaks: 7 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2926 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3242 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 385} Chain breaks: 5 Chain: "K" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2416 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 5, 'TRANS': 288} Chain: "L" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2420 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 918 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 738 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Q" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.78, per 1000 atoms: 0.59 Number of scatterers: 23310 At special positions: 0 Unit cell: (123.795, 159.165, 233.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 3 15.00 O 4322 8.00 N 3942 7.00 C 14912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 159 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 3.1 seconds 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 23 sheets defined 39.6% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.643A pdb=" N VAL A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 96 " --> pdb=" O LYS A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 96' Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.717A pdb=" N TRP A 182 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.402A pdb=" N THR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.926A pdb=" N ASP A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 762 through 769 removed outlier: 3.897A pdb=" N ASP A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.928A pdb=" N ALA A 781 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.635A pdb=" N VAL A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 809 " --> pdb=" O GLN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 928 removed outlier: 3.507A pdb=" N LEU A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.913A pdb=" N LYS A 940 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.529A pdb=" N THR A 956 " --> pdb=" O CYS A 952 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 958 " --> pdb=" O THR A 954 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 994 removed outlier: 5.107A pdb=" N GLN A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1186 removed outlier: 4.295A pdb=" N HIS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1223 through 1237 removed outlier: 3.734A pdb=" N ALA A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 3.517A pdb=" N ARG A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1291' Processing helix chain 'A' and resid 1309 through 1313 removed outlier: 3.565A pdb=" N LEU A1312 " --> pdb=" O PRO A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1411 Processing helix chain 'A' and resid 1445 through 1449 Processing helix chain 'A' and resid 1461 through 1463 No H-bonds generated for 'chain 'A' and resid 1461 through 1463' Processing helix chain 'A' and resid 1464 through 1480 Processing helix chain 'A' and resid 1567 through 1581 Processing helix chain 'A' and resid 1582 through 1584 No H-bonds generated for 'chain 'A' and resid 1582 through 1584' Processing helix chain 'A' and resid 1585 through 1596 Processing helix chain 'A' and resid 1597 through 1599 No H-bonds generated for 'chain 'A' and resid 1597 through 1599' Processing helix chain 'B' and resid 97 through 117 removed outlier: 4.343A pdb=" N ILE B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.900A pdb=" N PHE B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.562A pdb=" N ASP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.564A pdb=" N HIS B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 removed outlier: 4.047A pdb=" N ILE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 361 through 370 removed outlier: 5.004A pdb=" N GLU B 367 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.716A pdb=" N MET C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 80 " --> pdb=" O SER C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 80' Processing helix chain 'C' and resid 135 through 160 Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.156A pdb=" N ARG C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 removed outlier: 3.888A pdb=" N CYS C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 279 through 288 removed outlier: 3.563A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.596A pdb=" N GLY C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 4.128A pdb=" N GLN C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.527A pdb=" N GLU C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 removed outlier: 3.625A pdb=" N SER C 489 " --> pdb=" O ASN C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.551A pdb=" N ARG C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 516 removed outlier: 3.527A pdb=" N LEU C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 520 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 536 through 547 Processing helix chain 'C' and resid 558 through 564 removed outlier: 4.345A pdb=" N ALA C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 28 removed outlier: 4.208A pdb=" N ARG K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 66 through 76 Processing helix chain 'K' and resid 77 through 83 removed outlier: 3.538A pdb=" N PHE K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG K 83 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 117 Processing helix chain 'K' and resid 128 through 132 removed outlier: 4.159A pdb=" N LEU K 131 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 152 Processing helix chain 'K' and resid 167 through 181 removed outlier: 3.782A pdb=" N LYS K 171 " --> pdb=" O GLU K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 199 removed outlier: 3.691A pdb=" N LEU K 187 " --> pdb=" O ASN K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 243 Processing helix chain 'K' and resid 244 through 246 No H-bonds generated for 'chain 'K' and resid 244 through 246' Processing helix chain 'K' and resid 283 through 297 Processing helix chain 'L' and resid 73 through 86 removed outlier: 3.831A pdb=" N ILE L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 111 removed outlier: 3.842A pdb=" N SER L 105 " --> pdb=" O LYS L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 149 through 161 removed outlier: 4.612A pdb=" N HIS L 158 " --> pdb=" O LEU L 154 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE L 159 " --> pdb=" O THR L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 168 Processing helix chain 'L' and resid 184 through 199 Processing helix chain 'L' and resid 199 through 204 removed outlier: 3.658A pdb=" N ALA L 204 " --> pdb=" O ASN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 235 removed outlier: 4.054A pdb=" N ALA L 228 " --> pdb=" O SER L 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS L 235 " --> pdb=" O LYS L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 251 removed outlier: 3.566A pdb=" N LEU L 243 " --> pdb=" O GLN L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 300 removed outlier: 3.859A pdb=" N LEU L 284 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL L 295 " --> pdb=" O VAL L 291 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 358 removed outlier: 3.959A pdb=" N TYR L 354 " --> pdb=" O GLY L 350 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN L 355 " --> pdb=" O LEU L 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 64 Processing helix chain 'M' and resid 78 through 95 removed outlier: 3.709A pdb=" N ASP M 83 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU M 95 " --> pdb=" O ARG M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 120 removed outlier: 3.645A pdb=" N VAL M 118 " --> pdb=" O GLN M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 142 removed outlier: 3.515A pdb=" N LEU M 129 " --> pdb=" O PRO M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 43 through 45 No H-bonds generated for 'chain 'N' and resid 43 through 45' Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.988A pdb=" N SER N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA N 54 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 Processing helix chain 'N' and resid 117 through 124 Processing helix chain 'O' and resid 4 through 12 Processing helix chain 'O' and resid 13 through 16 Processing helix chain 'O' and resid 41 through 45 Processing helix chain 'O' and resid 46 through 60 removed outlier: 4.172A pdb=" N LEU O 50 " --> pdb=" O ARG O 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA O 56 " --> pdb=" O THR O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 110 Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 114 through 120 removed outlier: 3.520A pdb=" N ARG O 118 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN O 119 " --> pdb=" O GLU O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 12 removed outlier: 4.015A pdb=" N ILE P 12 " --> pdb=" O LEU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 51 Processing helix chain 'Q' and resid 2 through 13 removed outlier: 3.580A pdb=" N GLU Q 6 " --> pdb=" O GLU Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 53 removed outlier: 4.698A pdb=" N GLY Q 43 " --> pdb=" O ASP Q 39 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL Q 44 " --> pdb=" O GLU Q 40 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA Q 53 " --> pdb=" O ALA Q 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.900A pdb=" N ILE A 67 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER A 57 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 25 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.014A pdb=" N GLU A 101 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU A 144 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 99 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 100 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 163 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 367 removed outlier: 7.957A pdb=" N VAL A 364 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER A 333 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 366 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL A 335 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET A 170 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL A 334 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR A 172 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 336 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 174 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 255 " --> pdb=" O CYS A 893 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 4.286A pdb=" N ASP A 396 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 770 through 777 Processing sheet with id=AA7, first strand: chain 'A' and resid 1351 through 1357 removed outlier: 6.869A pdb=" N GLU A1385 " --> pdb=" O HIS A1375 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 945 " --> pdb=" O VAL A1419 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A1419 " --> pdb=" O ARG A 945 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1204 through 1206 Processing sheet with id=AA9, first strand: chain 'A' and resid 1254 through 1255 removed outlier: 6.824A pdb=" N ALA A1297 " --> pdb=" O PHE A1378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1439 through 1442 removed outlier: 5.212A pdb=" N VAL A1509 " --> pdb=" O HIS A1504 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A1501 " --> pdb=" O ASP A1485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 22 through 26 removed outlier: 5.051A pdb=" N ILE B 23 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 14 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE B 7 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP B 90 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 62 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 145 through 148 Processing sheet with id=AB4, first strand: chain 'B' and resid 174 through 177 Processing sheet with id=AB5, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AB6, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AB7, first strand: chain 'C' and resid 22 through 26 removed outlier: 4.703A pdb=" N LEU C 22 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 14 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 263 Processing sheet with id=AB9, first strand: chain 'C' and resid 372 through 373 removed outlier: 5.183A pdb=" N VAL C 333 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 45 through 52 removed outlier: 6.897A pdb=" N LYS K 8 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TRP K 61 " --> pdb=" O LYS K 8 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL K 10 " --> pdb=" O TRP K 61 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS K 63 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU K 12 " --> pdb=" O CYS K 63 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE K 122 " --> pdb=" O ALA K 158 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE K 160 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N CYS K 124 " --> pdb=" O PHE K 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 213 through 218 removed outlier: 6.867A pdb=" N VAL K 213 " --> pdb=" O GLU K 207 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU K 207 " --> pdb=" O VAL K 213 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.630A pdb=" N LEU L 65 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE L 141 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU L 140 " --> pdb=" O GLU L 174 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE L 176 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR L 142 " --> pdb=" O PHE L 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'N' and resid 31 through 36 removed outlier: 6.525A pdb=" N LEU N 24 " --> pdb=" O LEU N 32 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR N 34 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR N 22 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL N 81 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE O 72 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL O 80 " --> pdb=" O CYS O 73 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER O 95 " --> pdb=" O LEU O 19 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU O 19 " --> pdb=" O SER O 95 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE O 22 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS O 34 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL O 24 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 25 through 29 removed outlier: 6.588A pdb=" N VAL P 20 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER P 29 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR P 18 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS P 88 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR P 18 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL P 86 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL P 20 " --> pdb=" O VAL P 84 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL P 84 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG P 65 " --> pdb=" O GLU Q 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL Q 86 " --> pdb=" O MET Q 75 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN Q 77 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2697 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7565 1.35 - 1.48: 5839 1.48 - 1.61: 10202 1.61 - 1.74: 4 1.74 - 1.87: 197 Bond restraints: 23807 Sorted by residual: bond pdb=" C VAL A 733 " pdb=" N PRO A 734 " ideal model delta sigma weight residual 1.337 1.414 -0.077 9.80e-03 1.04e+04 6.22e+01 bond pdb=" C GLU N 117 " pdb=" N PRO N 118 " ideal model delta sigma weight residual 1.336 1.399 -0.064 1.23e-02 6.61e+03 2.67e+01 bond pdb=" C ASP L 125 " pdb=" N PRO L 126 " ideal model delta sigma weight residual 1.336 1.398 -0.062 1.23e-02 6.61e+03 2.54e+01 bond pdb=" N3B GNP K 500 " pdb=" PG GNP K 500 " ideal model delta sigma weight residual 1.801 1.703 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O5' GNP K 500 " pdb=" PA GNP K 500 " ideal model delta sigma weight residual 1.660 1.570 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 23802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 31443 3.34 - 6.69: 653 6.69 - 10.03: 131 10.03 - 13.38: 15 13.38 - 16.72: 6 Bond angle restraints: 32248 Sorted by residual: angle pdb=" C PHE K 52 " pdb=" N LEU K 53 " pdb=" CA LEU K 53 " ideal model delta sigma weight residual 122.46 130.46 -8.00 1.41e+00 5.03e-01 3.22e+01 angle pdb=" N VAL A 733 " pdb=" CA VAL A 733 " pdb=" C VAL A 733 " ideal model delta sigma weight residual 108.88 120.92 -12.04 2.16e+00 2.14e-01 3.11e+01 angle pdb=" C GLU C 226 " pdb=" N VAL C 227 " pdb=" CA VAL C 227 " ideal model delta sigma weight residual 120.62 129.73 -9.11 1.64e+00 3.72e-01 3.08e+01 angle pdb=" C GLU A 288 " pdb=" N GLN A 289 " pdb=" CA GLN A 289 " ideal model delta sigma weight residual 122.61 131.03 -8.42 1.56e+00 4.11e-01 2.91e+01 angle pdb=" CB MET K 252 " pdb=" CG MET K 252 " pdb=" SD MET K 252 " ideal model delta sigma weight residual 112.70 128.59 -15.89 3.00e+00 1.11e-01 2.81e+01 ... (remaining 32243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 12477 17.39 - 34.78: 1542 34.78 - 52.18: 260 52.18 - 69.57: 54 69.57 - 86.96: 26 Dihedral angle restraints: 14359 sinusoidal: 5830 harmonic: 8529 Sorted by residual: dihedral pdb=" CA VAL A 258 " pdb=" C VAL A 258 " pdb=" N VAL A 259 " pdb=" CA VAL A 259 " ideal model delta harmonic sigma weight residual -180.00 -123.04 -56.96 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA VAL N 86 " pdb=" C VAL N 86 " pdb=" N ALA N 87 " pdb=" CA ALA N 87 " ideal model delta harmonic sigma weight residual -180.00 -131.18 -48.82 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA VAL L 264 " pdb=" C VAL L 264 " pdb=" N VAL L 265 " pdb=" CA VAL L 265 " ideal model delta harmonic sigma weight residual -180.00 -140.70 -39.30 0 5.00e+00 4.00e-02 6.18e+01 ... (remaining 14356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3269 0.103 - 0.207: 348 0.207 - 0.310: 25 0.310 - 0.414: 3 0.414 - 0.517: 2 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CB ILE L 237 " pdb=" CA ILE L 237 " pdb=" CG1 ILE L 237 " pdb=" CG2 ILE L 237 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CB ILE K 181 " pdb=" CA ILE K 181 " pdb=" CG1 ILE K 181 " pdb=" CG2 ILE K 181 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 3644 not shown) Planarity restraints: 4109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 106 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" CG ASP A 106 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASP A 106 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP A 106 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 282 " -0.019 2.00e-02 2.50e+03 2.62e-02 1.21e+01 pdb=" CG PHE B 282 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 282 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 282 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 282 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 282 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 282 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 305 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ASN A 305 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN A 305 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR A 306 " 0.020 2.00e-02 2.50e+03 ... (remaining 4106 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4079 2.77 - 3.30: 21366 3.30 - 3.83: 39614 3.83 - 4.37: 43185 4.37 - 4.90: 72981 Nonbonded interactions: 181225 Sorted by model distance: nonbonded pdb=" OG1 THR A 864 " pdb=" OG1 THR A 871 " model vdw 2.234 3.040 nonbonded pdb=" O THR A 217 " pdb=" OG1 THR A 217 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 187 " pdb=" OE1 GLN B 188 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR P 74 " pdb=" OD1 ASN P 91 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR B 241 " pdb=" OE2 GLU B 310 " model vdw 2.287 3.040 ... (remaining 181220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 52.310 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23810 Z= 0.288 Angle : 1.198 16.722 32250 Z= 0.615 Chirality : 0.065 0.517 3647 Planarity : 0.007 0.069 4109 Dihedral : 15.610 86.959 8808 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.26 % Favored : 90.71 % Rotamer: Outliers : 0.04 % Allowed : 1.16 % Favored : 98.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.22 (0.14), residues: 2851 helix: -2.24 (0.13), residues: 1004 sheet: -1.38 (0.22), residues: 534 loop : -2.29 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP M 102 HIS 0.017 0.002 HIS A1375 PHE 0.060 0.003 PHE B 282 TYR 0.034 0.003 TYR B 351 ARG 0.018 0.001 ARG L 193 Details of bonding type rmsd hydrogen bonds : bond 0.14927 ( 960) hydrogen bonds : angle 7.64193 ( 2697) SS BOND : bond 0.01388 ( 1) SS BOND : angle 5.43554 ( 2) covalent geometry : bond 0.00611 (23807) covalent geometry : angle 1.19687 (32248) Misc. bond : bond 0.00442 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8596 (pmm) cc_final: 0.8258 (pmm) REVERT: B 255 VAL cc_start: 0.8637 (t) cc_final: 0.8220 (p) REVERT: B 319 MET cc_start: 0.8309 (mmp) cc_final: 0.8098 (mmm) REVERT: B 329 TYR cc_start: 0.7799 (m-80) cc_final: 0.7554 (m-80) REVERT: B 360 MET cc_start: 0.8202 (tpt) cc_final: 0.7965 (tpp) REVERT: C 79 MET cc_start: 0.8424 (mpp) cc_final: 0.8080 (mpp) REVERT: C 89 ASP cc_start: 0.8292 (p0) cc_final: 0.7842 (m-30) REVERT: C 90 ASN cc_start: 0.8696 (p0) cc_final: 0.8394 (p0) REVERT: C 308 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 368 PHE cc_start: 0.9245 (m-80) cc_final: 0.9043 (m-80) REVERT: K 139 LEU cc_start: 0.9398 (tt) cc_final: 0.9172 (mm) REVERT: K 273 MET cc_start: 0.9160 (tpt) cc_final: 0.8936 (tpt) REVERT: L 67 MET cc_start: 0.2687 (pmm) cc_final: 0.2263 (pmm) REVERT: L 192 GLN cc_start: 0.8921 (pp30) cc_final: 0.8491 (pp30) REVERT: L 288 MET cc_start: 0.9142 (tmm) cc_final: 0.8851 (tmm) REVERT: L 294 ASP cc_start: 0.8419 (p0) cc_final: 0.8197 (p0) REVERT: M 88 TYR cc_start: 0.7918 (m-10) cc_final: 0.7584 (m-80) REVERT: O 79 GLN cc_start: 0.7763 (mp10) cc_final: 0.7238 (mp10) REVERT: O 109 GLU cc_start: 0.8549 (tp30) cc_final: 0.7891 (pt0) REVERT: Q 24 THR cc_start: 0.7129 (t) cc_final: 0.6707 (t) REVERT: Q 37 LEU cc_start: 0.6536 (mt) cc_final: 0.6327 (mt) outliers start: 1 outliers final: 1 residues processed: 318 average time/residue: 0.3296 time to fit residues: 166.0395 Evaluate side-chains 229 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 chunk 73 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 115 optimal weight: 0.2980 chunk 223 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 overall best weight: 3.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN A 797 GLN A 809 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1216 ASN A1484 GLN B 205 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN L 83 HIS L 212 HIS ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN Q 7 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.091590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.071795 restraints weight = 108730.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070755 restraints weight = 62162.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.071396 restraints weight = 56870.112| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23810 Z= 0.196 Angle : 0.728 10.245 32250 Z= 0.380 Chirality : 0.046 0.197 3647 Planarity : 0.005 0.057 4109 Dihedral : 6.859 54.818 3162 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.93 % Favored : 92.04 % Rotamer: Outliers : 1.00 % Allowed : 10.07 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.14 (0.15), residues: 2851 helix: -0.71 (0.15), residues: 1010 sheet: -1.17 (0.23), residues: 517 loop : -2.06 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 379 HIS 0.008 0.001 HIS Q 79 PHE 0.023 0.002 PHE B 282 TYR 0.025 0.002 TYR L 299 ARG 0.005 0.000 ARG A 422 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 960) hydrogen bonds : angle 5.77862 ( 2697) SS BOND : bond 0.01491 ( 1) SS BOND : angle 2.15631 ( 2) covalent geometry : bond 0.00429 (23807) covalent geometry : angle 0.72760 (32248) Misc. bond : bond 0.00223 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8534 (pmm) cc_final: 0.8107 (pmm) REVERT: A 1553 MET cc_start: 0.8321 (ptm) cc_final: 0.7946 (ptp) REVERT: A 1598 MET cc_start: 0.7146 (ptp) cc_final: 0.6871 (ptp) REVERT: B 182 GLU cc_start: 0.8472 (pp20) cc_final: 0.8227 (pp20) REVERT: B 208 LYS cc_start: 0.5200 (OUTLIER) cc_final: 0.4518 (ttmt) REVERT: B 226 ASN cc_start: 0.8525 (t0) cc_final: 0.8240 (t0) REVERT: B 323 ILE cc_start: 0.9174 (mm) cc_final: 0.8792 (tp) REVERT: C 79 MET cc_start: 0.8456 (mpp) cc_final: 0.8251 (mpp) REVERT: C 125 ASN cc_start: 0.8332 (t0) cc_final: 0.7776 (m-40) REVERT: C 312 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8637 (pt) REVERT: K 23 MET cc_start: 0.8368 (ptp) cc_final: 0.7999 (mtt) REVERT: L 67 MET cc_start: 0.3088 (pmm) cc_final: 0.2883 (pmm) REVERT: L 132 MET cc_start: 0.8267 (ttt) cc_final: 0.7958 (tpp) REVERT: M 88 TYR cc_start: 0.8017 (m-10) cc_final: 0.7743 (m-80) REVERT: O 109 GLU cc_start: 0.8469 (tp30) cc_final: 0.8018 (pt0) outliers start: 26 outliers final: 12 residues processed: 259 average time/residue: 0.3185 time to fit residues: 135.2525 Evaluate side-chains 227 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain M residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 2 optimal weight: 4.9990 chunk 278 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 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 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 205 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.090276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068555 restraints weight = 109489.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068902 restraints weight = 62910.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068543 restraints weight = 52406.541| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 23810 Z= 0.240 Angle : 0.739 9.221 32250 Z= 0.383 Chirality : 0.046 0.189 3647 Planarity : 0.004 0.050 4109 Dihedral : 6.513 59.017 3160 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.91 % Favored : 91.06 % Rotamer: Outliers : 1.97 % Allowed : 13.70 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.81 (0.16), residues: 2851 helix: -0.24 (0.16), residues: 1011 sheet: -1.13 (0.23), residues: 523 loop : -1.97 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 379 HIS 0.013 0.001 HIS A 896 PHE 0.025 0.002 PHE B 11 TYR 0.023 0.002 TYR L 299 ARG 0.006 0.000 ARG L 193 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 960) hydrogen bonds : angle 5.70064 ( 2697) SS BOND : bond 0.00504 ( 1) SS BOND : angle 0.97299 ( 2) covalent geometry : bond 0.00526 (23807) covalent geometry : angle 0.73918 (32248) Misc. bond : bond 0.00208 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8990 (pmm) cc_final: 0.8320 (pmm) REVERT: A 802 PHE cc_start: 0.8998 (m-10) cc_final: 0.8780 (m-10) REVERT: B 208 LYS cc_start: 0.5203 (OUTLIER) cc_final: 0.4554 (ttmt) REVERT: B 226 ASN cc_start: 0.8817 (t160) cc_final: 0.8413 (t0) REVERT: B 319 MET cc_start: 0.8094 (mmp) cc_final: 0.7840 (mmm) REVERT: B 329 TYR cc_start: 0.8406 (m-80) cc_final: 0.8140 (m-80) REVERT: C 312 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8911 (pt) REVERT: C 393 MET cc_start: 0.9032 (mmm) cc_final: 0.8808 (mmp) REVERT: K 47 HIS cc_start: 0.9115 (OUTLIER) cc_final: 0.8806 (p-80) REVERT: L 132 MET cc_start: 0.8166 (ttt) cc_final: 0.7866 (tpp) REVERT: M 88 TYR cc_start: 0.7951 (m-10) cc_final: 0.7663 (m-80) REVERT: O 79 GLN cc_start: 0.7713 (mp10) cc_final: 0.7096 (mp10) REVERT: P 53 PHE cc_start: 0.5950 (t80) cc_final: 0.5716 (t80) outliers start: 51 outliers final: 32 residues processed: 255 average time/residue: 0.3181 time to fit residues: 133.4888 Evaluate side-chains 241 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 166 optimal weight: 30.0000 chunk 231 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 GLN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.089218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069428 restraints weight = 110065.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.068657 restraints weight = 62738.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069224 restraints weight = 58418.819| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 23810 Z= 0.247 Angle : 0.736 9.427 32250 Z= 0.381 Chirality : 0.046 0.185 3647 Planarity : 0.004 0.057 4109 Dihedral : 6.444 57.429 3160 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.01 % Favored : 90.95 % Rotamer: Outliers : 2.59 % Allowed : 16.17 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.75 (0.16), residues: 2851 helix: -0.10 (0.16), residues: 1024 sheet: -1.25 (0.23), residues: 530 loop : -1.97 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 379 HIS 0.014 0.001 HIS A1375 PHE 0.021 0.002 PHE K 259 TYR 0.028 0.002 TYR L 299 ARG 0.004 0.000 ARG L 193 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 960) hydrogen bonds : angle 5.70283 ( 2697) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.83350 ( 2) covalent geometry : bond 0.00543 (23807) covalent geometry : angle 0.73645 (32248) Misc. bond : bond 0.00210 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8064 (t0) cc_final: 0.7817 (t0) REVERT: A 856 MET cc_start: 0.8266 (tmm) cc_final: 0.8043 (tmm) REVERT: B 208 LYS cc_start: 0.5093 (OUTLIER) cc_final: 0.4379 (tttt) REVERT: B 226 ASN cc_start: 0.8644 (t160) cc_final: 0.8236 (t0) REVERT: B 323 ILE cc_start: 0.9198 (mm) cc_final: 0.8876 (tp) REVERT: C 312 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8686 (pt) REVERT: K 47 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8669 (p-80) REVERT: L 67 MET cc_start: 0.3150 (pmm) cc_final: 0.2699 (pmm) REVERT: L 132 MET cc_start: 0.8157 (ttt) cc_final: 0.7883 (tpp) REVERT: M 88 TYR cc_start: 0.7966 (m-10) cc_final: 0.7641 (m-80) REVERT: M 134 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6014 (pmt-80) REVERT: O 109 GLU cc_start: 0.8542 (tp30) cc_final: 0.8039 (tt0) REVERT: Q 30 ASN cc_start: 0.4387 (OUTLIER) cc_final: 0.4148 (p0) outliers start: 67 outliers final: 41 residues processed: 263 average time/residue: 0.3107 time to fit residues: 132.0829 Evaluate side-chains 248 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 14 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 274 optimal weight: 30.0000 chunk 218 optimal weight: 0.0570 chunk 39 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.090365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.070472 restraints weight = 109860.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069882 restraints weight = 61594.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070472 restraints weight = 55977.551| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23810 Z= 0.185 Angle : 0.699 10.140 32250 Z= 0.359 Chirality : 0.046 0.209 3647 Planarity : 0.004 0.054 4109 Dihedral : 6.219 56.288 3160 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.55 % Allowed : 18.02 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.60 (0.16), residues: 2851 helix: 0.05 (0.16), residues: 1023 sheet: -1.10 (0.23), residues: 514 loop : -1.93 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 379 HIS 0.011 0.001 HIS A1375 PHE 0.019 0.002 PHE C 124 TYR 0.033 0.002 TYR L 299 ARG 0.004 0.000 ARG O 85 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 960) hydrogen bonds : angle 5.58919 ( 2697) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.82585 ( 2) covalent geometry : bond 0.00410 (23807) covalent geometry : angle 0.69852 (32248) Misc. bond : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8445 (t0) cc_final: 0.8044 (t0) REVERT: A 856 MET cc_start: 0.8466 (tmm) cc_final: 0.8143 (tmm) REVERT: A 991 GLU cc_start: 0.8479 (pp20) cc_final: 0.7900 (pp20) REVERT: A 1598 MET cc_start: 0.7545 (ptp) cc_final: 0.7342 (ptp) REVERT: B 208 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4463 (tttt) REVERT: B 226 ASN cc_start: 0.8729 (t160) cc_final: 0.8238 (t0) REVERT: B 323 ILE cc_start: 0.9274 (mm) cc_final: 0.8901 (tp) REVERT: B 329 TYR cc_start: 0.8508 (m-80) cc_final: 0.8211 (m-80) REVERT: B 365 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8668 (tp) REVERT: C 312 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8794 (pt) REVERT: K 47 HIS cc_start: 0.9162 (OUTLIER) cc_final: 0.8727 (p-80) REVERT: L 67 MET cc_start: 0.2902 (pmm) cc_final: 0.2506 (pmm) REVERT: M 88 TYR cc_start: 0.7980 (m-10) cc_final: 0.7667 (m-80) REVERT: M 134 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6115 (pmt-80) REVERT: O 109 GLU cc_start: 0.8582 (tp30) cc_final: 0.8040 (tt0) REVERT: Q 30 ASN cc_start: 0.4602 (OUTLIER) cc_final: 0.4348 (p0) outliers start: 66 outliers final: 40 residues processed: 273 average time/residue: 0.4616 time to fit residues: 209.5055 Evaluate side-chains 251 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 207 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN A 797 GLN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 205 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS P 91 ASN Q 30 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.091457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071358 restraints weight = 108498.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.070639 restraints weight = 63413.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.071201 restraints weight = 50802.113| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23810 Z= 0.131 Angle : 0.671 11.443 32250 Z= 0.341 Chirality : 0.045 0.186 3647 Planarity : 0.004 0.053 4109 Dihedral : 5.870 55.404 3160 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.59 % Allowed : 19.07 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.39 (0.16), residues: 2851 helix: 0.31 (0.17), residues: 1014 sheet: -1.01 (0.23), residues: 505 loop : -1.87 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 379 HIS 0.010 0.001 HIS A1375 PHE 0.013 0.001 PHE K 206 TYR 0.025 0.001 TYR A 775 ARG 0.005 0.000 ARG A 422 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 960) hydrogen bonds : angle 5.35276 ( 2697) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.79726 ( 2) covalent geometry : bond 0.00293 (23807) covalent geometry : angle 0.67080 (32248) Misc. bond : bond 0.00163 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 MET cc_start: 0.8402 (tmm) cc_final: 0.8022 (tmm) REVERT: A 1553 MET cc_start: 0.8510 (ptm) cc_final: 0.8245 (ptt) REVERT: B 208 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.4772 (tttt) REVERT: B 329 TYR cc_start: 0.8529 (m-80) cc_final: 0.8251 (m-80) REVERT: C 125 ASN cc_start: 0.8349 (t0) cc_final: 0.7928 (m110) REVERT: C 312 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8857 (pt) REVERT: K 23 MET cc_start: 0.8574 (ptp) cc_final: 0.8285 (mtt) REVERT: K 47 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8317 (p-80) REVERT: K 168 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8122 (p) REVERT: L 67 MET cc_start: 0.2767 (pmm) cc_final: 0.2506 (pmm) REVERT: L 140 LEU cc_start: 0.8834 (mm) cc_final: 0.8630 (mm) REVERT: M 88 TYR cc_start: 0.7928 (m-10) cc_final: 0.7628 (m-80) REVERT: M 134 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6206 (pmt-80) REVERT: N 56 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: O 109 GLU cc_start: 0.8593 (tp30) cc_final: 0.8037 (tt0) REVERT: Q 75 MET cc_start: 0.7081 (mmt) cc_final: 0.6429 (mmp) outliers start: 67 outliers final: 38 residues processed: 292 average time/residue: 0.4246 time to fit residues: 204.9080 Evaluate side-chains 256 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 66 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 11 optimal weight: 0.0060 chunk 235 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 797 GLN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 226 ASN ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.089303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.069979 restraints weight = 108957.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068263 restraints weight = 70329.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068853 restraints weight = 60101.934| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 23810 Z= 0.228 Angle : 0.732 10.334 32250 Z= 0.376 Chirality : 0.047 0.196 3647 Planarity : 0.004 0.057 4109 Dihedral : 6.078 55.838 3160 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.74 % Allowed : 20.65 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.46 (0.16), residues: 2851 helix: 0.24 (0.16), residues: 1022 sheet: -1.08 (0.23), residues: 523 loop : -1.90 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1548 HIS 0.018 0.001 HIS A1375 PHE 0.021 0.002 PHE B 282 TYR 0.019 0.002 TYR L 282 ARG 0.004 0.000 ARG O 85 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 960) hydrogen bonds : angle 5.55484 ( 2697) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.86104 ( 2) covalent geometry : bond 0.00507 (23807) covalent geometry : angle 0.73155 (32248) Misc. bond : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 MET cc_start: 0.8490 (tmm) cc_final: 0.8104 (tmm) REVERT: B 78 ARG cc_start: 0.8456 (ptt-90) cc_final: 0.8093 (ptt-90) REVERT: B 208 LYS cc_start: 0.5355 (OUTLIER) cc_final: 0.4613 (tttt) REVERT: B 319 MET cc_start: 0.8362 (mmm) cc_final: 0.8142 (mmm) REVERT: B 323 ILE cc_start: 0.9266 (tp) cc_final: 0.8941 (tp) REVERT: B 365 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8695 (tp) REVERT: K 47 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8461 (p-80) REVERT: K 168 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (p) REVERT: L 67 MET cc_start: 0.2817 (pmm) cc_final: 0.2555 (pmm) REVERT: M 88 TYR cc_start: 0.7936 (m-10) cc_final: 0.7612 (m-80) REVERT: M 134 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6254 (pmt-80) REVERT: N 56 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7914 (m-10) REVERT: O 43 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.7298 (m90) REVERT: O 75 TYR cc_start: 0.7629 (m-80) cc_final: 0.7038 (m-10) REVERT: O 109 GLU cc_start: 0.8620 (tp30) cc_final: 0.8043 (tt0) outliers start: 71 outliers final: 53 residues processed: 254 average time/residue: 0.3197 time to fit residues: 132.7238 Evaluate side-chains 261 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 298 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 204 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 240 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 226 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.092162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.072301 restraints weight = 108907.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.071272 restraints weight = 65932.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071671 restraints weight = 54263.089| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23810 Z= 0.123 Angle : 0.700 15.699 32250 Z= 0.350 Chirality : 0.046 0.204 3647 Planarity : 0.003 0.052 4109 Dihedral : 5.709 54.617 3160 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.55 % Allowed : 21.65 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.24 (0.16), residues: 2851 helix: 0.42 (0.17), residues: 1008 sheet: -0.88 (0.23), residues: 510 loop : -1.79 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 102 HIS 0.014 0.001 HIS A1375 PHE 0.022 0.001 PHE A 802 TYR 0.022 0.001 TYR L 165 ARG 0.004 0.000 ARG A 422 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 960) hydrogen bonds : angle 5.30449 ( 2697) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.81466 ( 2) covalent geometry : bond 0.00272 (23807) covalent geometry : angle 0.69956 (32248) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 231 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 MET cc_start: 0.8229 (tmm) cc_final: 0.7870 (tmm) REVERT: A 1553 MET cc_start: 0.8379 (ptm) cc_final: 0.8140 (ptt) REVERT: B 137 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: B 208 LYS cc_start: 0.5502 (OUTLIER) cc_final: 0.4776 (tttt) REVERT: B 319 MET cc_start: 0.8404 (mmm) cc_final: 0.8159 (mmm) REVERT: B 323 ILE cc_start: 0.9203 (tp) cc_final: 0.8897 (tp) REVERT: B 329 TYR cc_start: 0.8422 (m-80) cc_final: 0.8202 (m-80) REVERT: C 125 ASN cc_start: 0.8299 (t0) cc_final: 0.7881 (m-40) REVERT: K 47 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.8129 (p-80) REVERT: K 168 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7959 (p) REVERT: L 130 TYR cc_start: 0.1904 (p90) cc_final: 0.1208 (m-10) REVERT: L 140 LEU cc_start: 0.8737 (mm) cc_final: 0.8497 (mm) REVERT: M 88 TYR cc_start: 0.7873 (m-10) cc_final: 0.7585 (m-80) REVERT: M 134 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6232 (pmt-80) REVERT: N 37 TYR cc_start: 0.5201 (p90) cc_final: 0.4886 (p90) REVERT: N 56 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: O 75 TYR cc_start: 0.7340 (m-80) cc_final: 0.6813 (m-80) REVERT: Q 75 MET cc_start: 0.7168 (mmt) cc_final: 0.6630 (mmp) outliers start: 66 outliers final: 40 residues processed: 278 average time/residue: 0.3199 time to fit residues: 144.5538 Evaluate side-chains 256 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 190 optimal weight: 0.8980 chunk 204 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 249 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 GLN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS M 130 GLN ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.092101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.072139 restraints weight = 108368.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071436 restraints weight = 61379.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071905 restraints weight = 52179.360| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 23810 Z= 0.131 Angle : 0.707 12.766 32250 Z= 0.353 Chirality : 0.046 0.207 3647 Planarity : 0.003 0.054 4109 Dihedral : 5.598 54.455 3160 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.28 % Allowed : 21.92 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.23 (0.16), residues: 2851 helix: 0.37 (0.17), residues: 1014 sheet: -0.80 (0.23), residues: 501 loop : -1.77 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 102 HIS 0.015 0.001 HIS A1375 PHE 0.039 0.001 PHE B 11 TYR 0.021 0.001 TYR A1465 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 960) hydrogen bonds : angle 5.34827 ( 2697) SS BOND : bond 0.00260 ( 1) SS BOND : angle 0.84760 ( 2) covalent geometry : bond 0.00297 (23807) covalent geometry : angle 0.70718 (32248) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8721 (ptp) cc_final: 0.8436 (pmm) REVERT: A 1553 MET cc_start: 0.8368 (ptm) cc_final: 0.8085 (ptt) REVERT: A 1598 MET cc_start: 0.8148 (pmm) cc_final: 0.7897 (pmm) REVERT: B 78 ARG cc_start: 0.8340 (ptt-90) cc_final: 0.8015 (ptt-90) REVERT: B 137 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: B 310 GLU cc_start: 0.8800 (pm20) cc_final: 0.8228 (pp20) REVERT: B 319 MET cc_start: 0.8482 (mmm) cc_final: 0.8209 (mmm) REVERT: B 323 ILE cc_start: 0.9245 (tp) cc_final: 0.8895 (tp) REVERT: B 329 TYR cc_start: 0.8425 (m-80) cc_final: 0.8167 (m-80) REVERT: C 125 ASN cc_start: 0.8390 (t0) cc_final: 0.8052 (m-40) REVERT: K 47 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8031 (p-80) REVERT: K 224 ASP cc_start: 0.8526 (p0) cc_final: 0.8280 (p0) REVERT: L 130 TYR cc_start: 0.1943 (p90) cc_final: 0.1199 (m-10) REVERT: M 88 TYR cc_start: 0.7868 (m-10) cc_final: 0.7575 (m-80) REVERT: M 134 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6292 (pmt-80) REVERT: N 37 TYR cc_start: 0.5199 (p90) cc_final: 0.4871 (p90) REVERT: N 56 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: O 75 TYR cc_start: 0.7551 (m-80) cc_final: 0.6972 (m-80) REVERT: O 109 GLU cc_start: 0.8670 (tp30) cc_final: 0.8089 (tt0) REVERT: Q 13 MET cc_start: 0.4578 (mtt) cc_final: 0.4374 (mtm) REVERT: Q 75 MET cc_start: 0.7046 (mmt) cc_final: 0.6497 (mmp) outliers start: 59 outliers final: 46 residues processed: 255 average time/residue: 0.3132 time to fit residues: 131.6607 Evaluate side-chains 254 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 152 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.089671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.070143 restraints weight = 109080.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068442 restraints weight = 72754.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.068745 restraints weight = 61848.014| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 23810 Z= 0.229 Angle : 0.764 13.072 32250 Z= 0.387 Chirality : 0.047 0.183 3647 Planarity : 0.004 0.059 4109 Dihedral : 5.882 54.313 3160 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.12 % Allowed : 22.00 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.38 (0.16), residues: 2851 helix: 0.30 (0.17), residues: 1015 sheet: -0.98 (0.23), residues: 503 loop : -1.85 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 102 HIS 0.021 0.001 HIS A1375 PHE 0.038 0.002 PHE N 101 TYR 0.019 0.002 TYR A 775 ARG 0.007 0.000 ARG L 193 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 960) hydrogen bonds : angle 5.53725 ( 2697) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.95984 ( 2) covalent geometry : bond 0.00509 (23807) covalent geometry : angle 0.76362 (32248) Misc. bond : bond 0.00200 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8951 (ptp) cc_final: 0.8541 (pmm) REVERT: A 180 GLU cc_start: 0.8127 (mp0) cc_final: 0.7841 (mp0) REVERT: A 1231 MET cc_start: 0.8734 (tpp) cc_final: 0.8531 (tpp) REVERT: A 1553 MET cc_start: 0.8576 (ptm) cc_final: 0.8017 (ptp) REVERT: A 1598 MET cc_start: 0.8263 (pmm) cc_final: 0.7964 (pmm) REVERT: B 78 ARG cc_start: 0.8435 (ptt-90) cc_final: 0.8097 (ptt-90) REVERT: B 137 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: B 323 ILE cc_start: 0.9318 (tp) cc_final: 0.8989 (tp) REVERT: B 329 TYR cc_start: 0.8460 (m-80) cc_final: 0.8148 (m-80) REVERT: K 47 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8207 (p-80) REVERT: K 168 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8201 (p) REVERT: L 67 MET cc_start: 0.4039 (pmm) cc_final: 0.2781 (pmm) REVERT: L 130 TYR cc_start: 0.2149 (p90) cc_final: 0.1278 (m-10) REVERT: M 88 TYR cc_start: 0.7968 (m-10) cc_final: 0.7666 (m-80) REVERT: M 134 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6321 (pmt-80) REVERT: N 56 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7734 (m-10) REVERT: O 75 TYR cc_start: 0.7616 (m-80) cc_final: 0.6972 (m-80) REVERT: O 109 GLU cc_start: 0.8663 (tp30) cc_final: 0.8122 (tt0) REVERT: Q 13 MET cc_start: 0.4782 (mtt) cc_final: 0.4555 (mtm) REVERT: Q 75 MET cc_start: 0.6943 (mmt) cc_final: 0.6394 (mmp) outliers start: 55 outliers final: 47 residues processed: 245 average time/residue: 0.3241 time to fit residues: 130.6504 Evaluate side-chains 250 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 30 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.090509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.071013 restraints weight = 108508.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.069483 restraints weight = 65953.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070150 restraints weight = 54165.816| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23810 Z= 0.171 Angle : 0.744 13.164 32250 Z= 0.373 Chirality : 0.046 0.244 3647 Planarity : 0.004 0.059 4109 Dihedral : 5.800 54.310 3160 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.16 % Allowed : 22.27 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.33 (0.16), residues: 2851 helix: 0.34 (0.17), residues: 1016 sheet: -0.95 (0.23), residues: 496 loop : -1.83 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP M 102 HIS 0.018 0.001 HIS A1375 PHE 0.037 0.002 PHE B 11 TYR 0.022 0.002 TYR B 230 ARG 0.008 0.000 ARG L 193 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 960) hydrogen bonds : angle 5.47250 ( 2697) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.95253 ( 2) covalent geometry : bond 0.00384 (23807) covalent geometry : angle 0.74374 (32248) Misc. bond : bond 0.00219 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7369.27 seconds wall clock time: 131 minutes 32.44 seconds (7892.44 seconds total)