Starting phenix.real_space_refine on Fri Mar 6 05:48:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8y_24249/03_2026/7n8y_24249.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8y_24249/03_2026/7n8y_24249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n8y_24249/03_2026/7n8y_24249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8y_24249/03_2026/7n8y_24249.map" model { file = "/net/cci-nas-00/data/ceres_data/7n8y_24249/03_2026/7n8y_24249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8y_24249/03_2026/7n8y_24249.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15708 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10199 2.51 5 N 2852 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16162 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1964 Classifications: {'peptide': 242} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 227} Chain: "B" Number of atoms: 6116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6116 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 759} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1964 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 227} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6118 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 759} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.88, per 1000 atoms: 0.24 Number of scatterers: 16162 At special positions: 0 Unit cell: (169.52, 142.48, 120.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3039 8.00 N 2852 7.00 C 10199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 716.0 milliseconds 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3820 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 32 sheets defined 25.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.014A pdb=" N THR A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 235 removed outlier: 4.364A pdb=" N THR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.705A pdb=" N ASN A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.566A pdb=" N PHE A 316 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 231 through 241 removed outlier: 4.183A pdb=" N LYS B 237 " --> pdb=" O TRP B 233 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 removed outlier: 4.146A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 4.059A pdb=" N HIS B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 4.161A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 382 removed outlier: 4.829A pdb=" N GLU B 374 " --> pdb=" O TYR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.837A pdb=" N ASP B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 4.329A pdb=" N GLU B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.866A pdb=" N VAL B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.979A pdb=" N VAL B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 626 removed outlier: 3.765A pdb=" N ALA B 623 " --> pdb=" O GLY B 619 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.515A pdb=" N ARG B 671 " --> pdb=" O GLU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 689 No H-bonds generated for 'chain 'B' and resid 687 through 689' Processing helix chain 'B' and resid 770 through 784 removed outlier: 3.604A pdb=" N ILE B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA B 775 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 776 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 789 removed outlier: 3.668A pdb=" N PHE B 789 " --> pdb=" O LYS B 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.015A pdb=" N THR C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 235 removed outlier: 4.365A pdb=" N THR C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.706A pdb=" N ASN C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.566A pdb=" N PHE C 316 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'D' and resid 4 through 12 removed outlier: 4.169A pdb=" N LEU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 4.072A pdb=" N ALA D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 29 removed outlier: 4.112A pdb=" N GLY D 29 " --> pdb=" O THR D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 26 through 29' Processing helix chain 'D' and resid 146 through 151 Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.831A pdb=" N CYS D 169 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D 170 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY D 171 " --> pdb=" O ASP D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 171' Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 231 through 240 removed outlier: 4.271A pdb=" N LYS D 237 " --> pdb=" O TRP D 233 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.763A pdb=" N VAL D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 369 through 384 removed outlier: 4.111A pdb=" N ARG D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 418 Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.765A pdb=" N ASP D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 4.271A pdb=" N GLU D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 503 removed outlier: 4.048A pdb=" N VAL D 498 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 525 removed outlier: 3.729A pdb=" N GLN D 522 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 524 " --> pdb=" O VAL D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 560 removed outlier: 4.391A pdb=" N ALA D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 613 through 626 removed outlier: 3.924A pdb=" N LEU D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 623 " --> pdb=" O GLY D 619 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 689 No H-bonds generated for 'chain 'D' and resid 687 through 689' Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 770 through 786 removed outlier: 3.765A pdb=" N ALA D 784 " --> pdb=" O LYS D 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 removed outlier: 6.213A pdb=" N THR A 126 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 193 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 206 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 295 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY A 292 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.405A pdb=" N THR B 157 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL B 35 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 159 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 31 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AA5, first strand: chain 'B' and resid 205 through 207 removed outlier: 3.621A pdb=" N ARG B 279 " --> pdb=" O VAL B 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 216 removed outlier: 3.529A pdb=" N VAL B 394 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 267 through 268 removed outlier: 3.648A pdb=" N ASP B 387 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 405 through 409 removed outlier: 3.642A pdb=" N ALA B 446 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 447 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 436 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 509 removed outlier: 6.531A pdb=" N GLN B 508 " --> pdb=" O PHE B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 515 through 516 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 574 Processing sheet with id=AB4, first strand: chain 'B' and resid 572 through 574 removed outlier: 3.575A pdb=" N VAL B 681 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N GLY B 660 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 10.289A pdb=" N SER B 649 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N ILE B 662 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N GLY B 647 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 664 " --> pdb=" O HIS B 645 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 577 through 578 Processing sheet with id=AB6, first strand: chain 'B' and resid 636 through 637 removed outlier: 3.759A pdb=" N LYS B 637 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.099A pdb=" N VAL B 736 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 761 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 738 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 759 " --> pdb=" O VAL B 738 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.099A pdb=" N VAL B 736 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 761 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 738 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 759 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 712 " --> pdb=" O LEU B 756 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 706 " --> pdb=" O LEU B 762 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 713 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 791 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.213A pdb=" N THR C 126 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 193 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 206 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 295 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY C 292 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AC2, first strand: chain 'D' and resid 2 through 3 removed outlier: 6.273A pdb=" N THR D 157 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D 35 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU D 159 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 161 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU D 31 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 43 through 47 removed outlier: 7.308A pdb=" N GLY D 44 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 94 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'D' and resid 205 through 207 removed outlier: 7.201A pdb=" N THR D 206 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N MET D 280 " --> pdb=" O THR D 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 279 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 215 through 216 Processing sheet with id=AC7, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AC8, first strand: chain 'D' and resid 286 through 288 Processing sheet with id=AC9, first strand: chain 'D' and resid 405 through 409 removed outlier: 3.670A pdb=" N ALA D 446 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 436 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 508 through 509 removed outlier: 6.181A pdb=" N GLN D 508 " --> pdb=" O PHE D 570 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR D 572 " --> pdb=" O GLN D 508 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 571 " --> pdb=" O ALA D 593 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE D 682 " --> pdb=" O GLY D 594 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 681 " --> pdb=" O GLY D 663 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 660 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 652 " --> pdb=" O GLY D 660 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 662 " --> pdb=" O ALA D 650 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN D 648 " --> pdb=" O VAL D 664 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 637 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 515 through 516 removed outlier: 4.588A pdb=" N LEU D 531 " --> pdb=" O MET D 544 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 577 through 578 Processing sheet with id=AD4, first strand: chain 'D' and resid 706 through 708 removed outlier: 3.670A pdb=" N GLY D 737 " --> pdb=" O ILE D 761 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 711 through 714 removed outlier: 3.786A pdb=" N VAL D 714 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 754 " --> pdb=" O VAL D 714 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1140 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: 2.76 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5100 1.33 - 1.45: 2377 1.45 - 1.57: 8875 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 16468 Sorted by residual: bond pdb=" N ILE C 185 " pdb=" CA ILE C 185 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.14e-02 7.69e+03 1.26e+01 bond pdb=" N ILE A 185 " pdb=" CA ILE A 185 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.15e-02 7.56e+03 1.12e+01 bond pdb=" N LEU B 673 " pdb=" CA LEU B 673 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.81e+00 bond pdb=" N GLN C 181 " pdb=" CA GLN C 181 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.98e+00 bond pdb=" CA THR B 628 " pdb=" C THR B 628 " ideal model delta sigma weight residual 1.523 1.561 -0.039 1.41e-02 5.03e+03 7.53e+00 ... (remaining 16463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 21518 2.28 - 4.55: 725 4.55 - 6.83: 59 6.83 - 9.10: 26 9.10 - 11.38: 11 Bond angle restraints: 22339 Sorted by residual: angle pdb=" N LYS B 688 " pdb=" CA LYS B 688 " pdb=" C LYS B 688 " ideal model delta sigma weight residual 114.56 107.65 6.91 1.27e+00 6.20e-01 2.96e+01 angle pdb=" N PRO C 183 " pdb=" CA PRO C 183 " pdb=" C PRO C 183 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.95e+01 angle pdb=" N PRO C 183 " pdb=" CA PRO C 183 " pdb=" CB PRO C 183 " ideal model delta sigma weight residual 103.08 98.08 5.00 9.70e-01 1.06e+00 2.66e+01 angle pdb=" N PRO C 184 " pdb=" CA PRO C 184 " pdb=" CB PRO C 184 " ideal model delta sigma weight residual 103.25 97.86 5.39 1.05e+00 9.07e-01 2.64e+01 angle pdb=" C ILE A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 127.00 138.38 -11.38 2.40e+00 1.74e-01 2.25e+01 ... (remaining 22334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.87: 9410 25.87 - 51.73: 506 51.73 - 77.60: 34 77.60 - 103.47: 6 103.47 - 129.33: 1 Dihedral angle restraints: 9957 sinusoidal: 4023 harmonic: 5934 Sorted by residual: dihedral pdb=" CA GLN C 182 " pdb=" C GLN C 182 " pdb=" N PRO C 183 " pdb=" CA PRO C 183 " ideal model delta harmonic sigma weight residual -180.00 -50.67 -129.33 0 5.00e+00 4.00e-02 6.69e+02 dihedral pdb=" CA THR D 196 " pdb=" C THR D 196 " pdb=" N ALA D 197 " pdb=" CA ALA D 197 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA VAL C 257 " pdb=" C VAL C 257 " pdb=" N ASP C 258 " pdb=" CA ASP C 258 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 9954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1754 0.052 - 0.104: 596 0.104 - 0.155: 132 0.155 - 0.207: 39 0.207 - 0.259: 11 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CB ILE B 634 " pdb=" CA ILE B 634 " pdb=" CG1 ILE B 634 " pdb=" CG2 ILE B 634 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB VAL B 612 " pdb=" CA VAL B 612 " pdb=" CG1 VAL B 612 " pdb=" CG2 VAL B 612 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE A 213 " pdb=" CA ILE A 213 " pdb=" CG1 ILE A 213 " pdb=" CG2 ILE A 213 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2529 not shown) Planarity restraints: 2945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 163 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO D 164 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 195 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C VAL D 195 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL D 195 " 0.019 2.00e-02 2.50e+03 pdb=" N THR D 196 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 672 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C LYS B 672 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS B 672 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 673 " -0.015 2.00e-02 2.50e+03 ... (remaining 2942 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4570 2.81 - 3.34: 13426 3.34 - 3.86: 24840 3.86 - 4.38: 27103 4.38 - 4.90: 48210 Nonbonded interactions: 118149 Sorted by model distance: nonbonded pdb=" OE1 GLU A 132 " pdb=" OH TYR A 194 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU C 132 " pdb=" OH TYR C 194 " model vdw 2.294 3.040 nonbonded pdb=" O ALA B 721 " pdb=" OG SER B 725 " model vdw 2.298 3.040 nonbonded pdb=" OD1 ASN B 325 " pdb=" OG1 THR B 328 " model vdw 2.304 3.040 nonbonded pdb=" O SER B 514 " pdb=" OG SER B 514 " model vdw 2.314 3.040 ... (remaining 118144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 791 or (resid 792 through 795 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 673 or (resid 674 and (name N or name CA or name \ C or name O or name CB )) or resid 675 through 795)) } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 15.350 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.005 0.082 16468 Z= 0.262 Angle : 0.984 11.379 22339 Z= 0.562 Chirality : 0.057 0.259 2532 Planarity : 0.007 0.074 2945 Dihedral : 14.983 129.332 6137 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.91 % Favored : 90.85 % Rotamer: Outliers : 0.69 % Allowed : 10.24 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.14), residues: 2066 helix: -3.32 (0.16), residues: 450 sheet: -4.10 (0.25), residues: 212 loop : -3.48 (0.13), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 148 TYR 0.019 0.002 TYR B 150 PHE 0.027 0.003 PHE C 293 TRP 0.010 0.001 TRP D 605 HIS 0.006 0.001 HIS D 666 Details of bonding type rmsd covalent geometry : bond 0.00537 (16468) covalent geometry : angle 0.98428 (22339) hydrogen bonds : bond 0.21604 ( 405) hydrogen bonds : angle 8.18803 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 272 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7367 (ttp-110) REVERT: A 182 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: A 196 ASN cc_start: 0.7573 (t0) cc_final: 0.7359 (t0) REVERT: A 274 MET cc_start: 0.7648 (mmm) cc_final: 0.7144 (mmm) REVERT: B 2 LYS cc_start: 0.7806 (ptpt) cc_final: 0.7565 (ptmm) REVERT: B 659 ILE cc_start: 0.8663 (tp) cc_final: 0.8306 (tp) REVERT: B 691 ASP cc_start: 0.7740 (p0) cc_final: 0.7177 (p0) REVERT: C 176 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7512 (ttp-110) REVERT: C 181 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: C 274 MET cc_start: 0.7508 (mmm) cc_final: 0.7084 (mmm) REVERT: D 19 ASP cc_start: 0.7269 (t0) cc_final: 0.7009 (t0) REVERT: D 251 ASP cc_start: 0.7110 (p0) cc_final: 0.6878 (p0) REVERT: D 362 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7685 (ptp-110) REVERT: D 424 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7469 (tm-30) REVERT: D 544 MET cc_start: 0.7756 (mmp) cc_final: 0.7436 (mmm) outliers start: 12 outliers final: 3 residues processed: 284 average time/residue: 0.1578 time to fit residues: 63.2386 Evaluate side-chains 185 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 180 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS A 222 ASN ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 156 ASN B 339 ASN B 480 GLN B 503 ASN B 581 GLN B 734 GLN B 766 ASN C 107 HIS C 139 ASN C 181 GLN C 196 ASN C 202 HIS C 222 ASN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 183 ASN D 254 ASN D 358 HIS D 588 GLN D 635 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.237199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.198181 restraints weight = 21977.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.198716 restraints weight = 14745.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.198955 restraints weight = 11914.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.200054 restraints weight = 10366.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.200425 restraints weight = 9483.582| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16468 Z= 0.127 Angle : 0.626 11.050 22339 Z= 0.328 Chirality : 0.045 0.183 2532 Planarity : 0.005 0.056 2945 Dihedral : 6.336 84.855 2265 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.34 % Favored : 90.61 % Rotamer: Outliers : 2.20 % Allowed : 15.97 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.15), residues: 2066 helix: -2.10 (0.21), residues: 464 sheet: -2.90 (0.28), residues: 256 loop : -3.18 (0.14), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 432 TYR 0.014 0.001 TYR C 247 PHE 0.020 0.001 PHE D 3 TRP 0.011 0.001 TRP B 444 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00287 (16468) covalent geometry : angle 0.62635 (22339) hydrogen bonds : bond 0.03795 ( 405) hydrogen bonds : angle 5.90537 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7490 (ttm110) cc_final: 0.7264 (ttp-110) REVERT: A 182 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: B 65 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6314 (p) REVERT: B 428 ASP cc_start: 0.7766 (t0) cc_final: 0.7445 (t0) REVERT: B 451 TRP cc_start: 0.8881 (p90) cc_final: 0.8265 (p90) REVERT: B 659 ILE cc_start: 0.8628 (tp) cc_final: 0.8325 (tp) REVERT: B 691 ASP cc_start: 0.7580 (p0) cc_final: 0.7136 (p0) REVERT: D 19 ASP cc_start: 0.7325 (t0) cc_final: 0.7011 (t0) REVERT: D 362 ARG cc_start: 0.8069 (ptp-170) cc_final: 0.7756 (ptp-110) REVERT: D 424 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7650 (tm-30) REVERT: D 451 TRP cc_start: 0.8945 (p90) cc_final: 0.8198 (p90) outliers start: 38 outliers final: 23 residues processed: 235 average time/residue: 0.1210 time to fit residues: 43.5499 Evaluate side-chains 194 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 662 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 420 HIS B 766 ASN C 196 ASN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 350 HIS D 564 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.228869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.195154 restraints weight = 21942.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.193794 restraints weight = 17692.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.194510 restraints weight = 14701.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.195620 restraints weight = 12204.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.195595 restraints weight = 11507.194| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16468 Z= 0.146 Angle : 0.616 10.456 22339 Z= 0.320 Chirality : 0.045 0.168 2532 Planarity : 0.005 0.071 2945 Dihedral : 5.958 82.260 2263 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.92 % Favored : 90.03 % Rotamer: Outliers : 2.72 % Allowed : 18.81 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.16), residues: 2066 helix: -1.57 (0.22), residues: 478 sheet: -2.66 (0.28), residues: 278 loop : -2.98 (0.15), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 359 TYR 0.015 0.001 TYR B 507 PHE 0.025 0.002 PHE A 230 TRP 0.010 0.001 TRP B 444 HIS 0.005 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00345 (16468) covalent geometry : angle 0.61575 (22339) hydrogen bonds : bond 0.03704 ( 405) hydrogen bonds : angle 5.67346 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: B 2 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7437 (ptmm) REVERT: B 65 THR cc_start: 0.7123 (OUTLIER) cc_final: 0.6701 (p) REVERT: B 659 ILE cc_start: 0.8718 (tp) cc_final: 0.8405 (tp) REVERT: B 691 ASP cc_start: 0.7347 (p0) cc_final: 0.7009 (p0) REVERT: D 19 ASP cc_start: 0.7278 (t0) cc_final: 0.6994 (t0) REVERT: D 424 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7441 (tm-30) REVERT: D 451 TRP cc_start: 0.8869 (p90) cc_final: 0.8280 (p90) REVERT: D 544 MET cc_start: 0.7526 (mmt) cc_final: 0.7281 (mmm) outliers start: 47 outliers final: 30 residues processed: 220 average time/residue: 0.1295 time to fit residues: 43.0364 Evaluate side-chains 196 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 117 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN B 766 ASN D 156 ASN ** D 521 GLN ** 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 = 0.4688 r_free = 0.4688 target = 0.222392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.188085 restraints weight = 21907.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186113 restraints weight = 18043.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.187058 restraints weight = 16690.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.188465 restraints weight = 13129.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188580 restraints weight = 10564.193| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16468 Z= 0.239 Angle : 0.706 12.013 22339 Z= 0.366 Chirality : 0.048 0.175 2532 Planarity : 0.005 0.060 2945 Dihedral : 6.306 88.758 2263 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 4.05 % Allowed : 19.27 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.16), residues: 2066 helix: -1.57 (0.22), residues: 466 sheet: -2.62 (0.27), residues: 302 loop : -2.87 (0.15), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 271 TYR 0.024 0.002 TYR B 507 PHE 0.024 0.002 PHE C 125 TRP 0.012 0.002 TRP A 266 HIS 0.006 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00572 (16468) covalent geometry : angle 0.70595 (22339) hydrogen bonds : bond 0.04134 ( 405) hydrogen bonds : angle 5.88501 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7384 (ttp-110) REVERT: A 182 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: B 2 LYS cc_start: 0.7811 (ptpt) cc_final: 0.7433 (ptmm) REVERT: B 65 THR cc_start: 0.7155 (OUTLIER) cc_final: 0.6740 (p) REVERT: B 432 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6904 (tmm-80) REVERT: B 455 MET cc_start: 0.7141 (ttm) cc_final: 0.6553 (ttp) REVERT: B 653 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6933 (m-10) REVERT: B 691 ASP cc_start: 0.7474 (p0) cc_final: 0.7190 (p0) REVERT: D 19 ASP cc_start: 0.7466 (t0) cc_final: 0.7161 (t0) REVERT: D 290 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5691 (tt) REVERT: D 424 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7525 (tm-30) REVERT: D 451 TRP cc_start: 0.8937 (p90) cc_final: 0.8265 (p90) REVERT: D 596 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7752 (pt) outliers start: 70 outliers final: 45 residues processed: 249 average time/residue: 0.1262 time to fit residues: 47.7726 Evaluate side-chains 220 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 57 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN B 766 ASN D 330 ASN ** D 588 GLN ** 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 = 0.4736 r_free = 0.4736 target = 0.227394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.196528 restraints weight = 21978.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.197947 restraints weight = 24408.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.197518 restraints weight = 15612.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.196764 restraints weight = 13937.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.197066 restraints weight = 12837.563| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16468 Z= 0.134 Angle : 0.598 9.492 22339 Z= 0.313 Chirality : 0.045 0.168 2532 Planarity : 0.004 0.053 2945 Dihedral : 5.445 59.268 2258 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 4.05 % Allowed : 20.31 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.17), residues: 2066 helix: -1.20 (0.23), residues: 476 sheet: -2.51 (0.27), residues: 306 loop : -2.72 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.013 0.001 TYR B 507 PHE 0.022 0.001 PHE A 230 TRP 0.009 0.001 TRP D 605 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00313 (16468) covalent geometry : angle 0.59845 (22339) hydrogen bonds : bond 0.03408 ( 405) hydrogen bonds : angle 5.50949 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 184 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: B 65 THR cc_start: 0.7211 (OUTLIER) cc_final: 0.6917 (p) REVERT: B 118 MET cc_start: 0.3439 (ptt) cc_final: 0.3117 (mtt) REVERT: B 455 MET cc_start: 0.7086 (ttm) cc_final: 0.6523 (ttp) REVERT: B 653 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6599 (m-10) REVERT: B 691 ASP cc_start: 0.7480 (p0) cc_final: 0.7073 (p0) REVERT: D 19 ASP cc_start: 0.7243 (t0) cc_final: 0.6956 (t0) REVERT: D 321 HIS cc_start: 0.6927 (t-170) cc_final: 0.6527 (t70) REVERT: D 424 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7455 (tm-30) REVERT: D 451 TRP cc_start: 0.8844 (p90) cc_final: 0.8290 (p90) REVERT: D 596 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7671 (pt) REVERT: D 653 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6928 (m-10) outliers start: 70 outliers final: 37 residues processed: 248 average time/residue: 0.1204 time to fit residues: 46.3891 Evaluate side-chains 214 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 182 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 180 optimal weight: 0.0470 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN D 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.227847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.196749 restraints weight = 22076.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.197070 restraints weight = 25800.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.198589 restraints weight = 17492.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.198257 restraints weight = 12446.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.198302 restraints weight = 13447.941| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16468 Z= 0.134 Angle : 0.597 12.649 22339 Z= 0.308 Chirality : 0.045 0.163 2532 Planarity : 0.004 0.048 2945 Dihedral : 5.286 58.890 2258 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 3.88 % Allowed : 19.97 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.17), residues: 2066 helix: -1.05 (0.23), residues: 480 sheet: -2.33 (0.26), residues: 336 loop : -2.64 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 432 TYR 0.014 0.001 TYR B 507 PHE 0.033 0.001 PHE D 317 TRP 0.007 0.001 TRP D 444 HIS 0.006 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00317 (16468) covalent geometry : angle 0.59737 (22339) hydrogen bonds : bond 0.03318 ( 405) hydrogen bonds : angle 5.38620 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 177 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7800 (t) REVERT: A 182 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: B 65 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6887 (p) REVERT: B 455 MET cc_start: 0.7072 (ttm) cc_final: 0.6537 (ttp) REVERT: B 591 MET cc_start: 0.6531 (mmm) cc_final: 0.6186 (mtp) REVERT: B 653 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6657 (m-10) REVERT: B 691 ASP cc_start: 0.7470 (p0) cc_final: 0.7039 (p0) REVERT: B 763 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: D 19 ASP cc_start: 0.7173 (t0) cc_final: 0.6906 (t0) REVERT: D 321 HIS cc_start: 0.6709 (t-170) cc_final: 0.6412 (t70) REVERT: D 424 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 451 TRP cc_start: 0.8837 (p90) cc_final: 0.8240 (p90) REVERT: D 596 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (pt) REVERT: D 653 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6958 (m-10) outliers start: 67 outliers final: 50 residues processed: 236 average time/residue: 0.1233 time to fit residues: 45.0946 Evaluate side-chains 221 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 144 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 154 optimal weight: 0.0270 chunk 50 optimal weight: 3.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN D 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.229386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.191062 restraints weight = 21930.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.189823 restraints weight = 17059.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.191024 restraints weight = 14765.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.192154 restraints weight = 12048.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.192493 restraints weight = 10094.592| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16468 Z= 0.193 Angle : 0.651 11.453 22339 Z= 0.336 Chirality : 0.046 0.159 2532 Planarity : 0.005 0.049 2945 Dihedral : 5.504 58.507 2258 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 4.57 % Allowed : 20.37 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.17), residues: 2066 helix: -1.09 (0.23), residues: 468 sheet: -2.37 (0.26), residues: 338 loop : -2.61 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 432 TYR 0.019 0.002 TYR B 507 PHE 0.025 0.002 PHE A 230 TRP 0.009 0.002 TRP C 266 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00461 (16468) covalent geometry : angle 0.65111 (22339) hydrogen bonds : bond 0.03696 ( 405) hydrogen bonds : angle 5.55157 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 176 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7815 (t) REVERT: A 176 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7382 (ttp-110) REVERT: A 182 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: B 65 THR cc_start: 0.7038 (OUTLIER) cc_final: 0.6729 (p) REVERT: B 455 MET cc_start: 0.6984 (ttm) cc_final: 0.6475 (ttp) REVERT: B 591 MET cc_start: 0.6768 (mmm) cc_final: 0.6325 (mtp) REVERT: B 653 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6857 (m-10) REVERT: B 691 ASP cc_start: 0.7563 (p0) cc_final: 0.7162 (p0) REVERT: B 703 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.4349 (m-80) REVERT: B 763 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: D 19 ASP cc_start: 0.7428 (t0) cc_final: 0.7151 (t0) REVERT: D 424 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7521 (tm-30) REVERT: D 451 TRP cc_start: 0.8912 (p90) cc_final: 0.8232 (p90) REVERT: D 596 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7724 (pt) REVERT: D 653 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6929 (m-10) REVERT: D 761 ILE cc_start: 0.3713 (OUTLIER) cc_final: 0.3225 (mp) outliers start: 79 outliers final: 55 residues processed: 245 average time/residue: 0.1179 time to fit residues: 45.0650 Evaluate side-chains 232 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 156 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 43 optimal weight: 0.0570 chunk 76 optimal weight: 0.1980 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** D 521 GLN ** 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 = 0.4733 r_free = 0.4733 target = 0.227251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.196397 restraints weight = 21884.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.197651 restraints weight = 25742.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.197195 restraints weight = 16115.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.196633 restraints weight = 14707.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.196794 restraints weight = 13400.444| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16468 Z= 0.139 Angle : 0.606 10.685 22339 Z= 0.314 Chirality : 0.045 0.174 2532 Planarity : 0.004 0.049 2945 Dihedral : 5.300 58.436 2258 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.22 % Allowed : 21.30 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.17), residues: 2066 helix: -0.96 (0.23), residues: 480 sheet: -2.20 (0.27), residues: 318 loop : -2.55 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 313 TYR 0.014 0.001 TYR B 507 PHE 0.025 0.002 PHE A 230 TRP 0.008 0.001 TRP D 318 HIS 0.006 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00327 (16468) covalent geometry : angle 0.60632 (22339) hydrogen bonds : bond 0.03312 ( 405) hydrogen bonds : angle 5.36781 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7817 (t) REVERT: A 176 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7353 (ttp-110) REVERT: A 182 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: B 182 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7691 (mm) REVERT: B 455 MET cc_start: 0.6966 (ttm) cc_final: 0.6490 (ttp) REVERT: B 509 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: B 591 MET cc_start: 0.6554 (mmm) cc_final: 0.6158 (mtp) REVERT: B 653 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6695 (m-10) REVERT: B 691 ASP cc_start: 0.7509 (p0) cc_final: 0.7099 (p0) REVERT: B 703 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.4121 (m-80) REVERT: B 763 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: D 19 ASP cc_start: 0.7282 (t0) cc_final: 0.7031 (t0) REVERT: D 222 LYS cc_start: 0.8090 (pttt) cc_final: 0.7775 (mttp) REVERT: D 424 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 596 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7662 (pt) REVERT: D 653 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.7010 (m-10) REVERT: D 761 ILE cc_start: 0.4101 (OUTLIER) cc_final: 0.3534 (mp) outliers start: 73 outliers final: 52 residues processed: 239 average time/residue: 0.1230 time to fit residues: 45.1148 Evaluate side-chains 229 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 204 optimal weight: 0.1980 chunk 111 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 42 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN B 766 ASN D 330 ASN D 369 GLN ** D 521 GLN ** 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 = 0.4748 r_free = 0.4748 target = 0.231186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.192929 restraints weight = 22020.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.191670 restraints weight = 16302.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.192611 restraints weight = 14481.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.193711 restraints weight = 11487.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.194011 restraints weight = 10107.082| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16468 Z= 0.159 Angle : 0.621 10.277 22339 Z= 0.320 Chirality : 0.045 0.157 2532 Planarity : 0.004 0.050 2945 Dihedral : 5.317 58.484 2258 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.17 % Allowed : 21.59 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.17), residues: 2066 helix: -0.97 (0.23), residues: 478 sheet: -2.27 (0.26), residues: 338 loop : -2.54 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 313 TYR 0.016 0.001 TYR B 507 PHE 0.024 0.002 PHE D 317 TRP 0.008 0.001 TRP D 11 HIS 0.006 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00378 (16468) covalent geometry : angle 0.62082 (22339) hydrogen bonds : bond 0.03430 ( 405) hydrogen bonds : angle 5.39619 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7831 (t) REVERT: A 176 ARG cc_start: 0.7615 (ttm110) cc_final: 0.7392 (ttp-110) REVERT: A 182 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: B 182 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7383 (mm) REVERT: B 455 MET cc_start: 0.6805 (ttm) cc_final: 0.6262 (ttp) REVERT: B 509 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: B 591 MET cc_start: 0.6685 (mmm) cc_final: 0.6279 (mtp) REVERT: B 653 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: B 691 ASP cc_start: 0.7547 (p0) cc_final: 0.7146 (p0) REVERT: B 703 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.4122 (m-80) REVERT: B 763 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: D 19 ASP cc_start: 0.7437 (t0) cc_final: 0.7159 (t0) REVERT: D 222 LYS cc_start: 0.8085 (pttt) cc_final: 0.7488 (mttt) REVERT: D 424 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7520 (tm-30) REVERT: D 451 TRP cc_start: 0.8907 (p90) cc_final: 0.8230 (p90) REVERT: D 596 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7776 (pt) REVERT: D 653 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6862 (m-10) REVERT: D 761 ILE cc_start: 0.3577 (OUTLIER) cc_final: 0.3133 (mp) outliers start: 72 outliers final: 57 residues processed: 238 average time/residue: 0.1222 time to fit residues: 44.2698 Evaluate side-chains 235 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 168 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 92 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 153 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.224062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189375 restraints weight = 21983.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188807 restraints weight = 17140.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.188689 restraints weight = 14764.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.189773 restraints weight = 13181.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.190059 restraints weight = 11373.191| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16468 Z= 0.189 Angle : 0.657 10.527 22339 Z= 0.338 Chirality : 0.046 0.153 2532 Planarity : 0.005 0.052 2945 Dihedral : 5.461 58.424 2258 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 4.22 % Allowed : 21.76 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.17), residues: 2066 helix: -1.00 (0.24), residues: 466 sheet: -2.30 (0.26), residues: 338 loop : -2.53 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 313 TYR 0.019 0.002 TYR B 507 PHE 0.026 0.002 PHE A 230 TRP 0.008 0.002 TRP B 451 HIS 0.006 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00454 (16468) covalent geometry : angle 0.65703 (22339) hydrogen bonds : bond 0.03650 ( 405) hydrogen bonds : angle 5.50510 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 170 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7819 (t) REVERT: A 176 ARG cc_start: 0.7602 (ttm110) cc_final: 0.7375 (ttp-110) REVERT: A 182 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: B 182 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7529 (mm) REVERT: B 455 MET cc_start: 0.6947 (ttm) cc_final: 0.6450 (ttp) REVERT: B 591 MET cc_start: 0.6759 (mmm) cc_final: 0.6326 (mtp) REVERT: B 653 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6838 (m-10) REVERT: B 691 ASP cc_start: 0.7562 (p0) cc_final: 0.7111 (p0) REVERT: B 703 PHE cc_start: 0.5683 (OUTLIER) cc_final: 0.4011 (m-80) REVERT: B 763 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: D 19 ASP cc_start: 0.7520 (t0) cc_final: 0.7251 (t0) REVERT: D 424 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7433 (tm-30) REVERT: D 451 TRP cc_start: 0.8867 (p90) cc_final: 0.8243 (p90) REVERT: D 596 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7716 (pt) REVERT: D 761 ILE cc_start: 0.3686 (OUTLIER) cc_final: 0.3184 (mp) outliers start: 73 outliers final: 60 residues processed: 234 average time/residue: 0.1073 time to fit residues: 39.0285 Evaluate side-chains 234 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 HIS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 766 ASN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 7 TRP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 761 ILE Chi-restraints excluded: chain D residue 789 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 169 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 179 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN B 766 ASN ** D 521 GLN ** 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 = 0.4741 r_free = 0.4741 target = 0.228267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.192093 restraints weight = 21727.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.192757 restraints weight = 14361.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.193234 restraints weight = 12355.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.194105 restraints weight = 10205.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.194629 restraints weight = 9551.998| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16468 Z= 0.122 Angle : 0.595 9.970 22339 Z= 0.306 Chirality : 0.044 0.156 2532 Planarity : 0.004 0.049 2945 Dihedral : 5.137 58.496 2258 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.94 % Allowed : 22.22 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.18), residues: 2066 helix: -0.80 (0.24), residues: 478 sheet: -2.22 (0.29), residues: 298 loop : -2.49 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 313 TYR 0.010 0.001 TYR B 507 PHE 0.024 0.001 PHE D 317 TRP 0.012 0.001 TRP D 318 HIS 0.006 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00286 (16468) covalent geometry : angle 0.59544 (22339) hydrogen bonds : bond 0.03131 ( 405) hydrogen bonds : angle 5.27232 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.29 seconds wall clock time: 46 minutes 13.46 seconds (2773.46 seconds total)