Starting phenix.real_space_refine on Mon Jul 6 16:34:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.map" model { file = "/net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fiz_31607/07_2026/7fiz_31607.cif" } resolution = 3.28 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= 0.001 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 136 5.16 5 C 23318 2.51 5 N 6485 2.21 5 O 7017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36970 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 727} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "S" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 111 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.82, per 1000 atoms: 0.21 Number of scatterers: 36970 At special positions: 0 Unit cell: (206.64, 205.82, 186.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 14 15.00 O 7017 8.00 N 6485 7.00 C 23318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.6 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 47 sheets defined 45.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.532A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.662A pdb=" N LEU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 138 removed outlier: 3.884A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.645A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 184 through 238 removed outlier: 4.457A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 259 through 275 removed outlier: 4.770A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.664A pdb=" N THR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.796A pdb=" N GLU B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 361 through 372 removed outlier: 3.661A pdb=" N GLY B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 removed outlier: 3.630A pdb=" N HIS B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.722A pdb=" N LEU B 440 " --> pdb=" O SER B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.983A pdb=" N ASN B 449 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.888A pdb=" N THR B 476 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 473 through 477' Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.170A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 514 removed outlier: 4.898A pdb=" N TRP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Proline residue: B 508 - end of helix removed outlier: 3.729A pdb=" N SER B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.875A pdb=" N GLU B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 removed outlier: 4.002A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 Processing helix chain 'B' and resid 680 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 4.145A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 Processing helix chain 'B' and resid 761 through 769 removed outlier: 4.419A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.601A pdb=" N ARG C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 139 removed outlier: 3.877A pdb=" N ALA C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 157 through 169 Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 184 through 236 Processing helix chain 'C' and resid 242 through 254 removed outlier: 4.235A pdb=" N GLU C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.687A pdb=" N ALA C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.645A pdb=" N LYS C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 removed outlier: 3.734A pdb=" N SER C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 removed outlier: 4.104A pdb=" N ILE C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 438 through 443 removed outlier: 4.162A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 506 through 515 removed outlier: 3.694A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 4.051A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 561 Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.668A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 647 through 652 removed outlier: 4.278A pdb=" N TYR C 651 " --> pdb=" O HIS C 647 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 647 through 652' Processing helix chain 'C' and resid 680 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.764A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 754 removed outlier: 3.755A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 754 " --> pdb=" O VAL C 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 749 through 754' Processing helix chain 'C' and resid 761 through 770 removed outlier: 4.177A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.781A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.632A pdb=" N LEU D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.532A pdb=" N LYS D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 236 removed outlier: 3.867A pdb=" N ARG D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 259 through 275 removed outlier: 4.486A pdb=" N ARG D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.959A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'D' and resid 363 through 372 removed outlier: 3.843A pdb=" N SER D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.521A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 427 removed outlier: 4.056A pdb=" N MET D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 424 through 427' Processing helix chain 'D' and resid 438 through 442 removed outlier: 3.874A pdb=" N GLU D 441 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 513 removed outlier: 4.293A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 534 Processing helix chain 'D' and resid 540 through 561 removed outlier: 3.530A pdb=" N GLY D 561 " --> pdb=" O PHE D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.680A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 647 Processing helix chain 'D' and resid 679 through 692 Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.979A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.935A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 769 removed outlier: 3.982A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 38 Processing helix chain 'E' and resid 58 through 60 No H-bonds generated for 'chain 'E' and resid 58 through 60' Processing helix chain 'E' and resid 117 through 139 Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.595A pdb=" N HIS E 168 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 169 " --> pdb=" O ILE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 Processing helix chain 'E' and resid 184 through 238 removed outlier: 3.675A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 228 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.848A pdb=" N VAL E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.659A pdb=" N GLU E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 322 through 339 removed outlier: 4.152A pdb=" N LYS E 326 " --> pdb=" O LEU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 373 Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.634A pdb=" N GLU E 389 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 434 through 439 removed outlier: 3.675A pdb=" N ALA E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 478 through 483 Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 506 through 514 Processing helix chain 'E' and resid 523 through 533 removed outlier: 3.701A pdb=" N ILE E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 561 Processing helix chain 'E' and resid 630 through 646 Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 729 removed outlier: 3.738A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY E 729 " --> pdb=" O ALA E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 746 removed outlier: 4.659A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN E 742 " --> pdb=" O ASN E 739 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU E 745 " --> pdb=" O GLN E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 752 Processing helix chain 'E' and resid 761 through 769 removed outlier: 4.176A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 removed outlier: 4.124A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 137 removed outlier: 4.325A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL F 136 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 removed outlier: 5.282A pdb=" N SER F 141 " --> pdb=" O ASN F 138 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG F 143 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 154 removed outlier: 4.018A pdb=" N GLY F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.752A pdb=" N ALA F 169 " --> pdb=" O ILE F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 182 Processing helix chain 'F' and resid 184 through 237 removed outlier: 3.791A pdb=" N ARG F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 245 Processing helix chain 'F' and resid 251 through 256 removed outlier: 3.579A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 268 removed outlier: 3.542A pdb=" N LYS F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 282 through 294 Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.536A pdb=" N THR F 311 " --> pdb=" O ASP F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 339 removed outlier: 4.112A pdb=" N TYR F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'F' and resid 403 through 411 removed outlier: 3.501A pdb=" N HIS F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 411 " --> pdb=" O HIS F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 444 removed outlier: 3.686A pdb=" N VAL F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 451 removed outlier: 3.763A pdb=" N ASN F 449 " --> pdb=" O GLU F 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR F 450 " --> pdb=" O GLN F 447 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE F 451 " --> pdb=" O ASN F 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 446 through 451' Processing helix chain 'F' and resid 479 through 484 removed outlier: 3.752A pdb=" N ARG F 484 " --> pdb=" O LEU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 506 through 513 Processing helix chain 'F' and resid 523 through 535 removed outlier: 4.293A pdb=" N THR F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 561 Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.844A pdb=" N ILE F 574 " --> pdb=" O ALA F 571 " (cutoff:3.500A) Proline residue: F 575 - end of helix Processing helix chain 'F' and resid 630 through 645 Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 727 removed outlier: 4.115A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 746 removed outlier: 4.284A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 761 through 767 removed outlier: 3.593A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 39 removed outlier: 4.342A pdb=" N ALA A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 117 through 139 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 169 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.553A pdb=" N LEU A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 241 removed outlier: 3.508A pdb=" N ARG A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 283 through 296 removed outlier: 3.634A pdb=" N ARG A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.524A pdb=" N ASP A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.778A pdb=" N LYS A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.942A pdb=" N GLU A 389 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.661A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 removed outlier: 4.061A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.578A pdb=" N LEU A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.605A pdb=" N ILE A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 4.164A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 680 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 4.275A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 742 through 746 removed outlier: 4.081A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.774A pdb=" N GLU A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 4.044A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.623A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 25 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 84 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 86 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYS B 72 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 90 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 67 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 46 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL B 47 " --> pdb=" O PRO B 6 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE B 8 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 5 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 379 removed outlier: 6.987A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASP B 422 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N THR B 470 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AA4, first strand: chain 'B' and resid 596 through 600 removed outlier: 4.012A pdb=" N VAL B 617 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.540A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 377 through 378 removed outlier: 7.089A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 351 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA C 471 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AB1, first strand: chain 'C' and resid 521 through 522 removed outlier: 7.584A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 596 through 603 removed outlier: 3.518A pdb=" N VAL C 617 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.743A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 705 through 706 Processing sheet with id=AB5, first strand: chain 'D' and resid 7 through 10 removed outlier: 3.542A pdb=" N VAL D 47 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 67 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA D 48 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N TRP D 65 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA D 74 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL D 84 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ARG D 76 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU D 82 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 82 " --> pdb=" O VAL D 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 7 through 10 removed outlier: 3.542A pdb=" N VAL D 47 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 67 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA D 48 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N TRP D 65 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA D 74 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL D 84 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ARG D 76 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU D 82 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG D 91 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.929A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 106 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 377 through 380 removed outlier: 6.516A pdb=" N HIS D 377 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP D 422 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 379 " --> pdb=" O ASP D 422 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU D 351 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA D 471 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU D 353 " --> pdb=" O ALA D 471 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE D 350 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 488 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 451 through 452 removed outlier: 3.545A pdb=" N PHE D 451 " --> pdb=" O TYR D 460 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.606A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 593 through 594 Processing sheet with id=AC3, first strand: chain 'D' and resid 596 through 597 removed outlier: 3.586A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D 662 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS D 622 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 663 " --> pdb=" O LYS D 622 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 601 through 603 removed outlier: 3.931A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.492A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 705 through 706 removed outlier: 3.780A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.758A pdb=" N LEU E 5 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG E 104 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR E 97 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG E 106 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 108 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN E 93 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE E 110 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG E 91 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR E 64 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ASP E 96 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N LEU E 62 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TRP E 65 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA E 48 " --> pdb=" O TRP E 65 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE E 44 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 20 through 25 Processing sheet with id=AC9, first strand: chain 'E' and resid 353 through 354 removed outlier: 3.558A pdb=" N ALA E 471 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 451 through 452 Processing sheet with id=AD2, first strand: chain 'E' and resid 521 through 522 removed outlier: 6.980A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 592 through 593 removed outlier: 3.557A pdb=" N GLN E 593 " --> pdb=" O ALA E 696 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 596 through 603 removed outlier: 3.658A pdb=" N THR E 603 " --> pdb=" O GLY E 606 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 606 " --> pdb=" O THR E 603 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 700 through 702 removed outlier: 3.547A pdb=" N ILE E 733 " --> pdb=" O GLU E 755 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 705 through 706 removed outlier: 3.836A pdb=" N GLU E 705 " --> pdb=" O MET E 713 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'F' and resid 20 through 23 removed outlier: 6.922A pdb=" N MET F 85 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 67 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.509A pdb=" N ARG F 91 " --> pdb=" O SER F 111 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 376 through 377 removed outlier: 6.689A pdb=" N HIS F 377 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU F 351 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA F 471 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.704A pdb=" N GLU F 521 " --> pdb=" O ILE F 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 596 through 601 removed outlier: 4.242A pdb=" N VAL F 617 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 732 through 736 Processing sheet with id=AE5, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.742A pdb=" N LEU A 5 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A 105 " --> pdb=" O LEU A 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'A' and resid 20 through 25 removed outlier: 8.047A pdb=" N GLN A 83 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA A 74 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET A 85 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN A 68 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG A 91 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 66 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 69 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 44 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 376 through 380 removed outlier: 7.091A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 351 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.994A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A' and resid 592 through 593 removed outlier: 3.959A pdb=" N GLN A 593 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 596 through 603 removed outlier: 3.848A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 664 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 617 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 662 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 700 through 701 removed outlier: 6.803A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) 1561 hydrogen bonds defined for protein. 4533 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: 7.77 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.28: 6398 1.28 - 1.44: 8905 1.44 - 1.61: 22074 1.61 - 1.78: 35 1.78 - 1.95: 233 Bond restraints: 37645 Sorted by residual: bond pdb=" C ALA F 679 " pdb=" O ALA F 679 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.19e-02 7.06e+03 1.20e+02 bond pdb=" C ASP A 675 " pdb=" O ASP A 675 " ideal model delta sigma weight residual 1.235 1.125 0.111 1.02e-02 9.61e+03 1.17e+02 bond pdb=" C ALA D 679 " pdb=" O ALA D 679 " ideal model delta sigma weight residual 1.233 1.108 0.125 1.30e-02 5.92e+03 9.27e+01 bond pdb=" C ASP E 675 " pdb=" O ASP E 675 " ideal model delta sigma weight residual 1.235 1.129 0.106 1.14e-02 7.69e+03 8.67e+01 bond pdb=" C ASP D 675 " pdb=" O ASP D 675 " ideal model delta sigma weight residual 1.234 1.123 0.111 1.20e-02 6.94e+03 8.53e+01 ... (remaining 37640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 50175 3.43 - 6.85: 783 6.85 - 10.28: 82 10.28 - 13.70: 13 13.70 - 17.13: 17 Bond angle restraints: 51070 Sorted by residual: angle pdb=" O ASP B 675 " pdb=" C ASP B 675 " pdb=" N GLY B 676 " ideal model delta sigma weight residual 123.42 106.29 17.13 1.07e+00 8.73e-01 2.56e+02 angle pdb=" O ASP A 675 " pdb=" C ASP A 675 " pdb=" N GLY A 676 " ideal model delta sigma weight residual 123.04 106.75 16.29 1.04e+00 9.25e-01 2.45e+02 angle pdb=" O ASP D 675 " pdb=" C ASP D 675 " pdb=" N GLY D 676 " ideal model delta sigma weight residual 123.42 107.21 16.21 1.07e+00 8.73e-01 2.30e+02 angle pdb=" O ALA F 679 " pdb=" C ALA F 679 " pdb=" N GLY F 680 " ideal model delta sigma weight residual 122.15 105.35 16.80 1.14e+00 7.69e-01 2.17e+02 angle pdb=" O ASP E 675 " pdb=" C ASP E 675 " pdb=" N GLY E 676 " ideal model delta sigma weight residual 123.31 106.58 16.73 1.17e+00 7.31e-01 2.05e+02 ... (remaining 51065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.79: 22811 27.79 - 55.58: 341 55.58 - 83.37: 60 83.37 - 111.16: 2 111.16 - 138.95: 4 Dihedral angle restraints: 23218 sinusoidal: 9659 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual -180.00 -99.39 -80.61 0 5.00e+00 4.00e-02 2.60e+02 dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -106.19 -73.81 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA GLU F 240 " pdb=" C GLU F 240 " pdb=" N ASP F 241 " pdb=" CA ASP F 241 " ideal model delta harmonic sigma weight residual 180.00 108.62 71.38 0 5.00e+00 4.00e-02 2.04e+02 ... (remaining 23215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5358 0.106 - 0.212: 452 0.212 - 0.318: 14 0.318 - 0.424: 3 0.424 - 0.530: 1 Chirality restraints: 5828 Sorted by residual: chirality pdb=" CA SER F 380 " pdb=" N SER F 380 " pdb=" C SER F 380 " pdb=" CB SER F 380 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA ARG B 385 " pdb=" N ARG B 385 " pdb=" C ARG B 385 " pdb=" CB ARG B 385 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CG LEU B 237 " pdb=" CB LEU B 237 " pdb=" CD1 LEU B 237 " pdb=" CD2 LEU B 237 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 5825 not shown) Planarity restraints: 6627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 679 " -0.091 2.00e-02 2.50e+03 1.78e-01 3.17e+02 pdb=" C ALA F 679 " 0.307 2.00e-02 2.50e+03 pdb=" O ALA F 679 " -0.130 2.00e-02 2.50e+03 pdb=" N GLY F 680 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 675 " -0.089 2.00e-02 2.50e+03 1.74e-01 3.04e+02 pdb=" C ASP B 675 " 0.300 2.00e-02 2.50e+03 pdb=" O ASP B 675 " -0.129 2.00e-02 2.50e+03 pdb=" N GLY B 676 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 679 " -0.090 2.00e-02 2.50e+03 1.74e-01 3.03e+02 pdb=" C ALA C 679 " 0.299 2.00e-02 2.50e+03 pdb=" O ALA C 679 " -0.132 2.00e-02 2.50e+03 pdb=" N GLY C 680 " -0.077 2.00e-02 2.50e+03 ... (remaining 6624 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4377 2.75 - 3.29: 34513 3.29 - 3.82: 60088 3.82 - 4.36: 70357 4.36 - 4.90: 119682 Nonbonded interactions: 289017 Sorted by model distance: nonbonded pdb=" OH TYR A 135 " pdb=" OD2 ASP A 199 " model vdw 2.212 3.040 nonbonded pdb=" O GLN F 278 " pdb=" OG SER F 280 " model vdw 2.221 3.040 nonbonded pdb=" O ASP B 422 " pdb=" OG1 THR B 470 " model vdw 2.229 3.040 nonbonded pdb=" O GLN D 234 " pdb=" OG SER D 244 " model vdw 2.230 3.040 nonbonded pdb=" O VAL B 359 " pdb=" O2B AGS B 901 " model vdw 2.257 3.040 ... (remaining 289012 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' and resid 2 through 780) selection = (chain 'B' and resid 2 through 780) selection = (chain 'C' and resid 2 through 780) selection = (chain 'D' and resid 2 through 780) selection = chain 'E' selection = (chain 'F' and resid 2 through 780) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.870 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.070 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 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 : 0.008 0.130 37645 Z= 0.411 Angle : 1.139 17.129 51070 Z= 0.664 Chirality : 0.060 0.530 5828 Planarity : 0.011 0.178 6627 Dihedral : 10.851 138.949 14486 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.93 % Favored : 92.86 % Rotamer: Outliers : 0.31 % Allowed : 3.23 % Favored : 96.46 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.25 % 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: -4.01 (0.10), residues: 4662 helix: -2.39 (0.09), residues: 1949 sheet: -2.52 (0.19), residues: 610 loop : -2.88 (0.11), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 227 TYR 0.048 0.003 TYR B 225 PHE 0.033 0.003 PHE C 45 TRP 0.027 0.003 TRP F 292 HIS 0.014 0.002 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.41 (37645) covalent geometry : angle 1.13892 / 0.66 (51070) hydrogen bonds : bond 0.17479 / 11.66 ( 1542) hydrogen bonds : angle 7.56716 / 5.42 ( 4533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 568 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 ILE cc_start: 0.8689 (pt) cc_final: 0.8486 (mp) REVERT: B 344 VAL cc_start: 0.9324 (m) cc_final: 0.8973 (t) REVERT: B 385 ARG cc_start: 0.8248 (ptt180) cc_final: 0.7812 (ptt90) REVERT: B 401 MET cc_start: 0.8315 (tpp) cc_final: 0.8059 (ttp) REVERT: B 612 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 282 GLU cc_start: 0.8326 (pt0) cc_final: 0.7950 (tp30) REVERT: C 432 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6271 (ttm110) REVERT: D 276 MET cc_start: 0.7886 (ptm) cc_final: 0.7541 (ptt) REVERT: D 423 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7782 (mm-30) REVERT: D 626 THR cc_start: 0.7506 (p) cc_final: 0.7185 (p) REVERT: E 351 LEU cc_start: 0.6890 (mt) cc_final: 0.6467 (mt) REVERT: E 387 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7993 (mp0) REVERT: E 466 PHE cc_start: 0.8032 (t80) cc_final: 0.7815 (t80) REVERT: E 485 MET cc_start: 0.8329 (mtt) cc_final: 0.8127 (mtt) REVERT: E 486 GLU cc_start: 0.7392 (tt0) cc_final: 0.6493 (tt0) REVERT: F 420 LEU cc_start: 0.7656 (tt) cc_final: 0.6952 (tp) REVERT: F 431 TRP cc_start: 0.6536 (p90) cc_final: 0.6324 (p-90) REVERT: F 456 LEU cc_start: 0.8019 (tp) cc_final: 0.7768 (tp) REVERT: F 516 MET cc_start: 0.8008 (mmm) cc_final: 0.7509 (mmm) REVERT: A 336 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8268 (mtt90) REVERT: A 401 MET cc_start: 0.7051 (tpt) cc_final: 0.6070 (tmm) REVERT: A 423 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7966 (mp0) REVERT: A 424 ILE cc_start: 0.8888 (pt) cc_final: 0.8641 (mt) REVERT: A 440 LEU cc_start: 0.8120 (tp) cc_final: 0.7880 (tp) REVERT: A 477 ILE cc_start: 0.8318 (mt) cc_final: 0.8010 (mp) outliers start: 12 outliers final: 4 residues processed: 577 average time/residue: 0.2485 time to fit residues: 221.6366 Evaluate side-chains 319 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 313 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 432 ARG Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain A residue 243 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 GLN B 411 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN C 138 ASN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 664 HIS C 731 HIS D 138 ASN D 407 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 HIS D 726 HIS E 177 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 220 ASN E 229 GLN E 234 GLN E 510 GLN E 647 HIS E 649 GLN E 727 GLN F 168 HIS ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN F 647 HIS ** F 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN A 139 HIS A 177 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.174180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129709 restraints weight = 118719.027| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.48 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37645 Z= 0.238 Angle : 0.759 24.228 51070 Z= 0.383 Chirality : 0.047 0.179 5828 Planarity : 0.006 0.084 6627 Dihedral : 8.127 140.750 5225 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.81 % Favored : 94.06 % Rotamer: Outliers : 1.96 % Allowed : 7.25 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.09 % 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: -2.69 (0.11), residues: 4662 helix: -0.80 (0.11), residues: 2014 sheet: -2.22 (0.19), residues: 640 loop : -2.63 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 693 TYR 0.024 0.002 TYR C 224 PHE 0.013 0.001 PHE E 451 TRP 0.024 0.002 TRP E 507 HIS 0.008 0.002 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (37645) covalent geometry : angle 0.75854 / 0.38 (51070) hydrogen bonds : bond 0.04677 / 3.10 ( 1542) hydrogen bonds : angle 5.57927 / 3.94 ( 4533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 314 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 ILE cc_start: 0.8659 (pt) cc_final: 0.8400 (mp) REVERT: B 343 ASP cc_start: 0.7163 (t70) cc_final: 0.6902 (t0) REVERT: B 385 ARG cc_start: 0.8068 (ptt180) cc_final: 0.7852 (ptt90) REVERT: B 612 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9065 (mp) REVERT: D 180 LEU cc_start: 0.1590 (OUTLIER) cc_final: 0.1178 (pt) REVERT: D 423 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 698 MET cc_start: 0.8822 (tpp) cc_final: 0.8604 (mmm) REVERT: D 719 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7514 (ptmm) REVERT: E 407 HIS cc_start: 0.8956 (m90) cc_final: 0.8702 (m90) REVERT: E 698 MET cc_start: 0.8744 (mmm) cc_final: 0.8527 (tpp) REVERT: F 217 MET cc_start: 0.3627 (tpt) cc_final: 0.2090 (ptt) REVERT: F 276 MET cc_start: 0.3097 (OUTLIER) cc_final: 0.2748 (pmm) REVERT: F 420 LEU cc_start: 0.7841 (tt) cc_final: 0.7619 (tt) REVERT: F 431 TRP cc_start: 0.6743 (p90) cc_final: 0.6328 (p-90) REVERT: F 516 MET cc_start: 0.7848 (mmm) cc_final: 0.7299 (mmt) REVERT: F 698 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7044 (mpp) REVERT: A 75 MET cc_start: 0.5897 (ptp) cc_final: 0.4760 (pmm) REVERT: A 160 MET cc_start: 0.0760 (ptm) cc_final: 0.0403 (ptm) REVERT: A 274 GLU cc_start: 0.8206 (tp30) cc_final: 0.7894 (mp0) REVERT: A 333 LEU cc_start: 0.8929 (mt) cc_final: 0.8700 (tt) REVERT: A 336 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8272 (mtm180) REVERT: A 401 MET cc_start: 0.8042 (tpt) cc_final: 0.7383 (tmm) REVERT: A 440 LEU cc_start: 0.8443 (tp) cc_final: 0.8134 (tp) REVERT: A 487 VAL cc_start: 0.9259 (m) cc_final: 0.9040 (t) outliers start: 77 outliers final: 38 residues processed: 373 average time/residue: 0.2139 time to fit residues: 129.3276 Evaluate side-chains 296 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 698 MET Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 218 optimal weight: 6.9990 chunk 389 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 344 optimal weight: 10.0000 chunk 431 optimal weight: 2.9990 chunk 167 optimal weight: 50.0000 chunk 0 optimal weight: 70.0000 chunk 182 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS C 211 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS E 628 GLN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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 = 0.4490 r_free = 0.4490 target = 0.174456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130133 restraints weight = 118384.330| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.59 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37645 Z= 0.166 Angle : 0.657 24.068 51070 Z= 0.328 Chirality : 0.044 0.175 5828 Planarity : 0.005 0.077 6627 Dihedral : 7.621 138.982 5217 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 2.09 % Allowed : 8.80 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 4662 helix: -0.07 (0.11), residues: 2037 sheet: -2.00 (0.19), residues: 647 loop : -2.41 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 328 TYR 0.022 0.001 TYR B 332 PHE 0.012 0.001 PHE C 45 TRP 0.016 0.001 TRP A 602 HIS 0.007 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (37645) covalent geometry : angle 0.65706 / 0.33 (51070) hydrogen bonds : bond 0.04102 / 2.73 ( 1542) hydrogen bonds : angle 5.06217 / 3.57 ( 4533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 291 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6781 (pp30) REVERT: B 308 ILE cc_start: 0.8522 (pt) cc_final: 0.8257 (mp) REVERT: B 343 ASP cc_start: 0.7089 (t70) cc_final: 0.6809 (t0) REVERT: B 612 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9011 (mp) REVERT: D 483 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8201 (t70) REVERT: D 698 MET cc_start: 0.8695 (tpp) cc_final: 0.8493 (mmm) REVERT: D 719 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7566 (ptmm) REVERT: E 401 MET cc_start: 0.7222 (mmm) cc_final: 0.6806 (mmm) REVERT: E 407 HIS cc_start: 0.8955 (m90) cc_final: 0.8641 (m90) REVERT: E 674 LYS cc_start: 0.6266 (OUTLIER) cc_final: 0.6055 (mtmt) REVERT: E 698 MET cc_start: 0.8681 (mmm) cc_final: 0.8453 (tpp) REVERT: F 227 ARG cc_start: 0.6591 (mmt180) cc_final: 0.6084 (mmt180) REVERT: F 276 MET cc_start: 0.2991 (OUTLIER) cc_final: 0.2607 (pmm) REVERT: F 406 ILE cc_start: 0.9363 (mm) cc_final: 0.9140 (tp) REVERT: F 431 TRP cc_start: 0.6533 (p90) cc_final: 0.6243 (p-90) REVERT: F 516 MET cc_start: 0.7962 (mmm) cc_final: 0.7417 (mmm) REVERT: F 635 GLU cc_start: 0.8070 (pt0) cc_final: 0.7795 (mt-10) REVERT: F 644 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 75 MET cc_start: 0.6049 (ptp) cc_final: 0.4940 (pmm) REVERT: A 85 MET cc_start: 0.4517 (OUTLIER) cc_final: 0.4308 (tpt) REVERT: A 160 MET cc_start: 0.0553 (ptm) cc_final: 0.0202 (ptm) REVERT: A 274 GLU cc_start: 0.8201 (tp30) cc_final: 0.7908 (mp0) REVERT: A 333 LEU cc_start: 0.8980 (mt) cc_final: 0.8769 (tt) REVERT: A 336 ARG cc_start: 0.8537 (mtt180) cc_final: 0.8141 (mtm180) REVERT: A 401 MET cc_start: 0.8019 (tpt) cc_final: 0.7267 (tmm) outliers start: 82 outliers final: 46 residues processed: 350 average time/residue: 0.2042 time to fit residues: 118.1127 Evaluate side-chains 312 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 258 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 698 MET Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 111 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 362 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 331 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 407 HIS B 411 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS E 220 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN F 447 GLN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN A 373 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.172751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126615 restraints weight = 114789.987| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 5.19 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 37645 Z= 0.241 Angle : 0.719 23.324 51070 Z= 0.358 Chirality : 0.046 0.168 5828 Planarity : 0.006 0.071 6627 Dihedral : 7.577 139.361 5217 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.86 % Favored : 93.03 % Rotamer: Outliers : 2.72 % Allowed : 10.18 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.12), residues: 4662 helix: 0.17 (0.11), residues: 2038 sheet: -1.83 (0.19), residues: 631 loop : -2.29 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 328 TYR 0.024 0.002 TYR B 332 PHE 0.016 0.002 PHE F 467 TRP 0.013 0.002 TRP C 431 HIS 0.008 0.001 HIS E 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (37645) covalent geometry : angle 0.71885 / 0.36 (51070) hydrogen bonds : bond 0.04349 / 2.91 ( 1542) hydrogen bonds : angle 4.97650 / 3.50 ( 4533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 272 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 ILE cc_start: 0.8515 (pt) cc_final: 0.8210 (mp) REVERT: B 343 ASP cc_start: 0.7087 (t70) cc_final: 0.6747 (t0) REVERT: B 394 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6893 (pmm150) REVERT: B 776 MET cc_start: 0.8235 (ttt) cc_final: 0.7904 (ttp) REVERT: C 287 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8200 (tpt-90) REVERT: D 180 LEU cc_start: 0.1500 (OUTLIER) cc_final: 0.1171 (pt) REVERT: D 483 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8494 (t70) REVERT: D 698 MET cc_start: 0.8813 (tpp) cc_final: 0.8504 (mmm) REVERT: E 401 MET cc_start: 0.7427 (mmm) cc_final: 0.7005 (mmm) REVERT: E 407 HIS cc_start: 0.9012 (m90) cc_final: 0.8691 (m90) REVERT: E 674 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5989 (mtmt) REVERT: F 217 MET cc_start: 0.3518 (tpt) cc_final: 0.1974 (ptt) REVERT: F 401 MET cc_start: 0.6707 (ptt) cc_final: 0.6433 (ptt) REVERT: F 406 ILE cc_start: 0.9335 (mm) cc_final: 0.9079 (tp) REVERT: F 431 TRP cc_start: 0.6510 (p90) cc_final: 0.6186 (p-90) REVERT: F 516 MET cc_start: 0.8164 (mmm) cc_final: 0.7840 (mmp) REVERT: F 644 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8546 (mp) REVERT: F 698 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6710 (mpp) REVERT: F 776 MET cc_start: 0.5808 (mtt) cc_final: 0.5528 (mpp) REVERT: A 75 MET cc_start: 0.6127 (ptp) cc_final: 0.5150 (pmm) REVERT: A 160 MET cc_start: 0.0471 (ptm) cc_final: 0.0099 (ptp) REVERT: A 274 GLU cc_start: 0.8059 (tp30) cc_final: 0.7801 (mp0) REVERT: A 336 ARG cc_start: 0.8499 (mtt180) cc_final: 0.8002 (mtm-85) REVERT: A 352 VAL cc_start: 0.9162 (t) cc_final: 0.8907 (p) REVERT: A 486 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8125 (mm-30) outliers start: 107 outliers final: 68 residues processed: 351 average time/residue: 0.2210 time to fit residues: 129.0866 Evaluate side-chains 328 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 253 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 698 MET Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 80 optimal weight: 40.0000 chunk 452 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 404 optimal weight: 8.9990 chunk 445 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 443 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 324 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS D 168 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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 = 0.4443 r_free = 0.4443 target = 0.171776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127485 restraints weight = 115850.026| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 5.28 r_work: 0.3410 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 37645 Z= 0.284 Angle : 0.741 22.268 51070 Z= 0.371 Chirality : 0.047 0.245 5828 Planarity : 0.006 0.070 6627 Dihedral : 7.602 140.194 5215 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 3.08 % Allowed : 10.99 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4662 helix: 0.20 (0.11), residues: 2038 sheet: -1.85 (0.20), residues: 622 loop : -2.28 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.028 0.002 TYR D 534 PHE 0.015 0.002 PHE E 467 TRP 0.017 0.002 TRP A 602 HIS 0.009 0.001 HIS E 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 (37645) covalent geometry : angle 0.74110 / 0.37 (51070) hydrogen bonds : bond 0.04438 / 2.95 ( 1542) hydrogen bonds : angle 5.03495 / 3.54 ( 4533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 260 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4319 (ptp) REVERT: B 343 ASP cc_start: 0.7398 (t70) cc_final: 0.7035 (t0) REVERT: B 394 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7933 (pmm150) REVERT: C 287 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8339 (tpt-90) REVERT: C 537 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: D 180 LEU cc_start: 0.1594 (OUTLIER) cc_final: 0.1242 (pt) REVERT: D 249 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8384 (tt) REVERT: D 483 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8642 (t70) REVERT: E 401 MET cc_start: 0.7737 (mmm) cc_final: 0.7357 (mmm) REVERT: E 407 HIS cc_start: 0.9055 (m90) cc_final: 0.8765 (m90) REVERT: F 401 MET cc_start: 0.6834 (ptt) cc_final: 0.6522 (ptt) REVERT: F 431 TRP cc_start: 0.6527 (p90) cc_final: 0.6153 (p-90) REVERT: F 516 MET cc_start: 0.8337 (mmm) cc_final: 0.8011 (mmp) REVERT: F 587 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8761 (ptmt) REVERT: F 644 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8502 (mp) REVERT: F 698 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.6972 (mpp) REVERT: A 75 MET cc_start: 0.6301 (ptp) cc_final: 0.5213 (pmm) REVERT: A 160 MET cc_start: 0.0486 (ptm) cc_final: 0.0057 (ptp) REVERT: A 274 GLU cc_start: 0.8182 (tp30) cc_final: 0.7826 (mp0) REVERT: A 302 ASP cc_start: 0.8012 (m-30) cc_final: 0.7279 (p0) REVERT: A 336 ARG cc_start: 0.8861 (mtt180) cc_final: 0.8328 (mtm-85) REVERT: A 352 VAL cc_start: 0.9177 (t) cc_final: 0.8885 (p) REVERT: A 486 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8687 (mm-30) outliers start: 121 outliers final: 84 residues processed: 348 average time/residue: 0.2028 time to fit residues: 118.8819 Evaluate side-chains 338 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 245 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 698 MET Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 379 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 221 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 chunk 395 optimal weight: 20.0000 chunk 425 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 chunk 416 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 416 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 727 GLN ** A 447 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 = 0.4466 r_free = 0.4466 target = 0.173400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.127817 restraints weight = 115312.635| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 4.61 r_work: 0.3450 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37645 Z= 0.155 Angle : 0.629 22.113 51070 Z= 0.313 Chirality : 0.044 0.199 5828 Planarity : 0.005 0.067 6627 Dihedral : 7.222 139.734 5211 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.57 % Allowed : 11.70 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 4662 helix: 0.56 (0.12), residues: 2038 sheet: -1.61 (0.20), residues: 609 loop : -2.11 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.020 0.001 TYR B 332 PHE 0.013 0.001 PHE F 467 TRP 0.021 0.001 TRP A 602 HIS 0.010 0.001 HIS D 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (37645) covalent geometry : angle 0.62902 / 0.31 (51070) hydrogen bonds : bond 0.03724 / 2.48 ( 1542) hydrogen bonds : angle 4.67817 / 3.29 ( 4533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 261 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 252 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8736 (tptp) REVERT: B 343 ASP cc_start: 0.7297 (t70) cc_final: 0.6849 (t0) REVERT: B 394 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7727 (pmm150) REVERT: C 287 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8190 (tpt-90) REVERT: D 180 LEU cc_start: 0.1431 (OUTLIER) cc_final: 0.1096 (pt) REVERT: D 423 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8079 (tp30) REVERT: D 483 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8483 (t70) REVERT: D 698 MET cc_start: 0.8720 (tpp) cc_final: 0.8384 (mmm) REVERT: E 407 HIS cc_start: 0.8968 (m90) cc_final: 0.8678 (m90) REVERT: E 628 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8672 (mm110) REVERT: E 691 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8951 (mp) REVERT: E 698 MET cc_start: 0.8902 (mmm) cc_final: 0.8664 (tpp) REVERT: E 749 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6139 (tm-30) REVERT: F 427 MET cc_start: 0.8194 (mmt) cc_final: 0.7808 (mmm) REVERT: F 431 TRP cc_start: 0.6564 (p90) cc_final: 0.6171 (p-90) REVERT: F 587 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8780 (ptmt) REVERT: F 644 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 75 MET cc_start: 0.6177 (ptp) cc_final: 0.5249 (pmm) REVERT: A 160 MET cc_start: 0.0426 (ptm) cc_final: -0.0018 (ptp) REVERT: A 258 MET cc_start: 0.6955 (mpt) cc_final: 0.6522 (mpt) REVERT: A 274 GLU cc_start: 0.8032 (tp30) cc_final: 0.7759 (mp0) REVERT: A 302 ASP cc_start: 0.7860 (m-30) cc_final: 0.7278 (p0) REVERT: A 336 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8320 (mtm-85) REVERT: A 352 VAL cc_start: 0.9171 (t) cc_final: 0.8865 (p) REVERT: A 486 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8566 (mm-30) REVERT: A 535 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9046 (p) REVERT: A 633 MET cc_start: 0.8963 (tpp) cc_final: 0.8458 (ttm) outliers start: 101 outliers final: 68 residues processed: 337 average time/residue: 0.2023 time to fit residues: 116.0120 Evaluate side-chains 325 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 248 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 749 GLU Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 254 optimal weight: 30.0000 chunk 368 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 401 optimal weight: 2.9990 chunk 422 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 79 optimal weight: 50.0000 chunk 141 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 435 optimal weight: 4.9990 chunk 376 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 416 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN ** A 447 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 = 0.4459 r_free = 0.4459 target = 0.173079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127828 restraints weight = 115028.284| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.48 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37645 Z= 0.165 Angle : 0.637 21.485 51070 Z= 0.315 Chirality : 0.044 0.197 5828 Planarity : 0.005 0.086 6627 Dihedral : 7.129 138.737 5211 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 2.82 % Allowed : 11.73 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.12), residues: 4662 helix: 0.67 (0.12), residues: 2048 sheet: -1.53 (0.20), residues: 605 loop : -2.02 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 545 TYR 0.026 0.001 TYR D 534 PHE 0.023 0.001 PHE E 657 TRP 0.017 0.001 TRP A 602 HIS 0.008 0.001 HIS D 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (37645) covalent geometry : angle 0.63675 / 0.31 (51070) hydrogen bonds : bond 0.03693 / 2.46 ( 1542) hydrogen bonds : angle 4.60247 / 3.23 ( 4533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 253 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 ASP cc_start: 0.7046 (t70) cc_final: 0.6674 (t0) REVERT: B 394 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6889 (pmm150) REVERT: B 612 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8988 (mp) REVERT: C 120 VAL cc_start: 0.0950 (OUTLIER) cc_final: 0.0713 (m) REVERT: C 230 MET cc_start: 0.7165 (ptt) cc_final: 0.6911 (mtt) REVERT: C 287 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7840 (tpt-90) REVERT: C 773 GLU cc_start: 0.5919 (pm20) cc_final: 0.5610 (pm20) REVERT: D 180 LEU cc_start: 0.1461 (OUTLIER) cc_final: 0.1097 (pt) REVERT: D 423 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7511 (tp30) REVERT: D 483 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8321 (t70) REVERT: E 407 HIS cc_start: 0.8920 (m90) cc_final: 0.8610 (m90) REVERT: E 516 MET cc_start: 0.7250 (tpp) cc_final: 0.7007 (tpp) REVERT: E 691 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8963 (mp) REVERT: E 698 MET cc_start: 0.8755 (mmm) cc_final: 0.8514 (tpp) REVERT: E 749 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6018 (tm-30) REVERT: F 217 MET cc_start: 0.3469 (tpt) cc_final: 0.2103 (ptt) REVERT: F 431 TRP cc_start: 0.6565 (p90) cc_final: 0.6210 (p-90) REVERT: F 516 MET cc_start: 0.8235 (mmp) cc_final: 0.7912 (mmm) REVERT: F 644 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8484 (mp) REVERT: F 776 MET cc_start: 0.5737 (mtm) cc_final: 0.5448 (mpp) REVERT: A 75 MET cc_start: 0.6326 (ptp) cc_final: 0.5285 (pmm) REVERT: A 160 MET cc_start: 0.0464 (ptm) cc_final: 0.0159 (ptm) REVERT: A 274 GLU cc_start: 0.8148 (tp30) cc_final: 0.7824 (mp0) REVERT: A 336 ARG cc_start: 0.8368 (mtt180) cc_final: 0.8004 (mtm180) REVERT: A 352 VAL cc_start: 0.9167 (t) cc_final: 0.8904 (p) REVERT: A 486 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: A 516 MET cc_start: 0.8306 (mmm) cc_final: 0.8093 (mtp) REVERT: A 535 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8838 (p) REVERT: A 633 MET cc_start: 0.8661 (tpp) cc_final: 0.8261 (ttm) outliers start: 111 outliers final: 75 residues processed: 334 average time/residue: 0.2007 time to fit residues: 113.7970 Evaluate side-chains 328 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 749 GLU Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 253 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 368 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 79 optimal weight: 50.0000 chunk 332 optimal weight: 30.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 416 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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 = 0.4464 r_free = 0.4464 target = 0.173356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.128075 restraints weight = 114390.010| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 4.54 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37645 Z= 0.148 Angle : 0.621 20.309 51070 Z= 0.306 Chirality : 0.043 0.195 5828 Planarity : 0.005 0.090 6627 Dihedral : 7.020 137.969 5211 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 2.62 % Allowed : 12.06 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4662 helix: 0.84 (0.12), residues: 2040 sheet: -1.46 (0.20), residues: 605 loop : -1.97 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 545 TYR 0.021 0.001 TYR D 534 PHE 0.036 0.001 PHE F 467 TRP 0.017 0.001 TRP A 602 HIS 0.006 0.001 HIS D 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (37645) covalent geometry : angle 0.62131 / 0.31 (51070) hydrogen bonds : bond 0.03534 / 2.36 ( 1542) hydrogen bonds : angle 4.49422 / 3.15 ( 4533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 254 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 ASP cc_start: 0.7104 (t70) cc_final: 0.6667 (t0) REVERT: B 394 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6967 (pmm150) REVERT: B 612 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8999 (mp) REVERT: C 120 VAL cc_start: 0.0937 (OUTLIER) cc_final: 0.0697 (m) REVERT: C 287 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7791 (tpt-90) REVERT: C 773 GLU cc_start: 0.5735 (pm20) cc_final: 0.5489 (pm20) REVERT: D 180 LEU cc_start: 0.1464 (OUTLIER) cc_final: 0.1099 (pt) REVERT: D 483 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8323 (t70) REVERT: E 227 ARG cc_start: 0.6623 (mmt90) cc_final: 0.5977 (mtt-85) REVERT: E 407 HIS cc_start: 0.8880 (m90) cc_final: 0.8585 (m90) REVERT: E 516 MET cc_start: 0.7230 (tpp) cc_final: 0.6974 (tpp) REVERT: E 628 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8305 (mm-40) REVERT: E 691 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8951 (mp) REVERT: E 698 MET cc_start: 0.8759 (mmm) cc_final: 0.8507 (tpp) REVERT: E 749 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5965 (tm-30) REVERT: F 431 TRP cc_start: 0.6614 (p90) cc_final: 0.6260 (p-90) REVERT: F 516 MET cc_start: 0.8261 (mmp) cc_final: 0.7978 (mmm) REVERT: F 644 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 75 MET cc_start: 0.6403 (ptp) cc_final: 0.5336 (pmm) REVERT: A 160 MET cc_start: 0.0397 (ptm) cc_final: 0.0083 (ptm) REVERT: A 258 MET cc_start: 0.6786 (mpt) cc_final: 0.6189 (mpt) REVERT: A 274 GLU cc_start: 0.8171 (tp30) cc_final: 0.7831 (mp0) REVERT: A 336 ARG cc_start: 0.8430 (mtt180) cc_final: 0.8041 (mtm180) REVERT: A 352 VAL cc_start: 0.9189 (t) cc_final: 0.8934 (p) REVERT: A 486 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8232 (mm-30) REVERT: A 516 MET cc_start: 0.8295 (mmm) cc_final: 0.8002 (mtp) outliers start: 103 outliers final: 73 residues processed: 330 average time/residue: 0.2018 time to fit residues: 112.0692 Evaluate side-chains 334 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 251 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 749 GLU Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 314 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 229 optimal weight: 5.9990 chunk 451 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 334 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 242 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 416 ASN C 68 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 664 HIS ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.171752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.125995 restraints weight = 115170.476| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.38 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 37645 Z= 0.238 Angle : 0.694 19.913 51070 Z= 0.344 Chirality : 0.045 0.194 5828 Planarity : 0.005 0.092 6627 Dihedral : 7.167 137.215 5211 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.44 % Favored : 92.49 % Rotamer: Outliers : 2.47 % Allowed : 12.52 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 4662 helix: 0.68 (0.12), residues: 2052 sheet: -1.50 (0.21), residues: 593 loop : -2.04 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 272 TYR 0.022 0.002 TYR B 332 PHE 0.019 0.002 PHE E 657 TRP 0.020 0.002 TRP E 431 HIS 0.010 0.001 HIS D 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (37645) covalent geometry : angle 0.69417 / 0.34 (51070) hydrogen bonds : bond 0.04005 / 2.67 ( 1542) hydrogen bonds : angle 4.68327 / 3.28 ( 4533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 256 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 ASP cc_start: 0.7210 (t70) cc_final: 0.6699 (t0) REVERT: B 612 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9032 (mp) REVERT: C 120 VAL cc_start: 0.0833 (OUTLIER) cc_final: 0.0589 (m) REVERT: C 287 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8166 (tpt-90) REVERT: D 180 LEU cc_start: 0.1517 (OUTLIER) cc_final: 0.1141 (pt) REVERT: D 423 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7648 (tp30) REVERT: D 483 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8504 (t70) REVERT: D 698 MET cc_start: 0.8832 (mmm) cc_final: 0.8619 (mmm) REVERT: E 227 ARG cc_start: 0.6716 (mmt90) cc_final: 0.5867 (mtm-85) REVERT: E 407 HIS cc_start: 0.8903 (m90) cc_final: 0.8584 (m90) REVERT: E 516 MET cc_start: 0.7267 (tpp) cc_final: 0.6993 (tpp) REVERT: E 628 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8375 (mm-40) REVERT: E 691 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8924 (mp) REVERT: E 749 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6501 (mt-10) REVERT: F 418 VAL cc_start: 0.8703 (m) cc_final: 0.8503 (t) REVERT: F 427 MET cc_start: 0.8167 (mmt) cc_final: 0.7744 (mmm) REVERT: F 431 TRP cc_start: 0.6702 (p90) cc_final: 0.6370 (p-90) REVERT: F 644 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8497 (mp) REVERT: F 776 MET cc_start: 0.5821 (mtm) cc_final: 0.5255 (mpp) REVERT: A 75 MET cc_start: 0.6477 (ptp) cc_final: 0.5272 (pmm) REVERT: A 160 MET cc_start: 0.0449 (ptm) cc_final: 0.0017 (ptp) REVERT: A 258 MET cc_start: 0.6816 (mpt) cc_final: 0.6243 (mpt) REVERT: A 274 GLU cc_start: 0.8171 (tp30) cc_final: 0.7838 (mp0) REVERT: A 336 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7960 (mtm-85) REVERT: A 352 VAL cc_start: 0.9192 (t) cc_final: 0.8914 (p) REVERT: A 422 ASP cc_start: 0.8442 (t0) cc_final: 0.7916 (p0) REVERT: A 486 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: A 516 MET cc_start: 0.8363 (mmm) cc_final: 0.8009 (mtp) REVERT: A 633 MET cc_start: 0.8658 (tpp) cc_final: 0.8389 (ttm) outliers start: 97 outliers final: 78 residues processed: 327 average time/residue: 0.2055 time to fit residues: 113.4262 Evaluate side-chains 338 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 251 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 749 GLU Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 87 optimal weight: 40.0000 chunk 102 optimal weight: 5.9990 chunk 167 optimal weight: 40.0000 chunk 368 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 386 optimal weight: 30.0000 chunk 394 optimal weight: 8.9990 chunk 324 optimal weight: 0.7980 chunk 252 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 419 optimal weight: 20.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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 = 0.4436 r_free = 0.4436 target = 0.171760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126552 restraints weight = 115485.181| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 5.30 r_work: 0.3397 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 37645 Z= 0.229 Angle : 0.698 19.432 51070 Z= 0.346 Chirality : 0.045 0.203 5828 Planarity : 0.005 0.093 6627 Dihedral : 7.179 136.943 5211 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 2.49 % Allowed : 12.82 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.12), residues: 4662 helix: 0.66 (0.12), residues: 2052 sheet: -1.55 (0.20), residues: 609 loop : -2.03 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 545 TYR 0.021 0.002 TYR B 332 PHE 0.036 0.002 PHE F 467 TRP 0.021 0.002 TRP E 431 HIS 0.009 0.001 HIS D 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (37645) covalent geometry : angle 0.69774 / 0.35 (51070) hydrogen bonds : bond 0.03970 / 2.65 ( 1542) hydrogen bonds : angle 4.69609 / 3.29 ( 4533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 252 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 252 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8710 (tptp) REVERT: B 612 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9076 (mp) REVERT: C 120 VAL cc_start: 0.0990 (OUTLIER) cc_final: 0.0744 (m) REVERT: C 287 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8231 (tpt-90) REVERT: D 180 LEU cc_start: 0.1455 (OUTLIER) cc_final: 0.1098 (pt) REVERT: D 483 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8460 (t70) REVERT: E 227 ARG cc_start: 0.6675 (mmt90) cc_final: 0.5882 (mtm-85) REVERT: E 407 HIS cc_start: 0.8968 (m90) cc_final: 0.8672 (m90) REVERT: E 516 MET cc_start: 0.7471 (tpp) cc_final: 0.7172 (tpp) REVERT: E 628 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8564 (mm-40) REVERT: E 691 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8928 (mp) REVERT: E 749 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: F 75 MET cc_start: -0.0314 (tmm) cc_final: -0.0527 (ttm) REVERT: F 427 MET cc_start: 0.8272 (mmt) cc_final: 0.7863 (mmm) REVERT: F 431 TRP cc_start: 0.6654 (p90) cc_final: 0.6320 (p-90) REVERT: F 644 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8453 (mp) REVERT: F 776 MET cc_start: 0.5983 (mtm) cc_final: 0.5468 (mpp) REVERT: A 75 MET cc_start: 0.6353 (ptp) cc_final: 0.5307 (pmm) REVERT: A 160 MET cc_start: 0.0329 (ptm) cc_final: -0.0059 (ptp) REVERT: A 258 MET cc_start: 0.6940 (mpt) cc_final: 0.6472 (mpt) REVERT: A 274 GLU cc_start: 0.8014 (tp30) cc_final: 0.7701 (mp0) REVERT: A 352 VAL cc_start: 0.9230 (t) cc_final: 0.8923 (p) REVERT: A 422 ASP cc_start: 0.8668 (t0) cc_final: 0.8039 (p0) REVERT: A 486 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8697 (mt-10) REVERT: A 516 MET cc_start: 0.8617 (mmm) cc_final: 0.8256 (mtp) REVERT: A 633 MET cc_start: 0.9014 (tpp) cc_final: 0.8735 (ttm) outliers start: 98 outliers final: 83 residues processed: 324 average time/residue: 0.1961 time to fit residues: 108.7372 Evaluate side-chains 339 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 246 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 749 GLU Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 382 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 171 optimal weight: 40.0000 chunk 316 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 246 optimal weight: 30.0000 chunk 250 optimal weight: 50.0000 chunk 31 optimal weight: 8.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 416 ASN B 628 GLN C 49 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS D 168 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.170613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120388 restraints weight = 113373.532| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 5.36 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 37645 Z= 0.324 Angle : 0.819 19.221 51070 Z= 0.407 Chirality : 0.049 0.242 5828 Planarity : 0.006 0.093 6627 Dihedral : 7.505 136.120 5211 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.05 % Favored : 90.88 % Rotamer: Outliers : 2.44 % Allowed : 13.08 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.12), residues: 4662 helix: 0.33 (0.11), residues: 2042 sheet: -1.77 (0.20), residues: 621 loop : -2.15 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 328 TYR 0.025 0.002 TYR B 332 PHE 0.041 0.002 PHE F 467 TRP 0.039 0.002 TRP E 431 HIS 0.012 0.002 HIS D 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.32 (37645) covalent geometry : angle 0.81866 / 0.41 (51070) hydrogen bonds : bond 0.04644 / 3.11 ( 1542) hydrogen bonds : angle 5.03932 / 3.54 ( 4533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11166.27 seconds wall clock time: 191 minutes 2.33 seconds (11462.33 seconds total)