Starting phenix.real_space_refine on Mon Jun 23 14:55:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8u_15240/06_2025/8a8u_15240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8u_15240/06_2025/8a8u_15240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a8u_15240/06_2025/8a8u_15240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8u_15240/06_2025/8a8u_15240.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8u_15240/06_2025/8a8u_15240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8u_15240/06_2025/8a8u_15240.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.058 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 20 5.49 5 S 66 5.16 5 C 17023 2.51 5 N 4833 2.21 5 O 5187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27129 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4403 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 540} Chain breaks: 4 Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4483 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 548} Chain breaks: 3 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4510 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 553} Chain breaks: 2 Chain: "D" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4530 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 555} Chain breaks: 2 Chain: "E" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4490 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 548} Chain breaks: 3 Chain: "F" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4329 Classifications: {'peptide': 546} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 527} Chain breaks: 5 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.34, per 1000 atoms: 0.64 Number of scatterers: 27129 At special positions: 0 Unit cell: (119.7, 135.09, 150.48, 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 66 16.00 P 20 15.00 O 5187 8.00 N 4833 7.00 C 17023 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: 6.88 Conformation dependent library (CDL) restraints added in 3.5 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 28 sheets defined 59.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.860A pdb=" N VAL A 293 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 371 removed outlier: 4.608A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 4.053A pdb=" N ARG A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 415 removed outlier: 4.150A pdb=" N MET A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 removed outlier: 3.676A pdb=" N ILE A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.796A pdb=" N LEU A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.512A pdb=" N ARG A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 690 through 705 Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.725A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 772 through 781 removed outlier: 3.800A pdb=" N GLN A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 779 " --> pdb=" O ARG A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.631A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.769A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.672A pdb=" N VAL B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.575A pdb=" N VAL B 293 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.598A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.958A pdb=" N ARG B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 371 removed outlier: 4.890A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 Processing helix chain 'B' and resid 396 through 415 Processing helix chain 'B' and resid 480 through 493 Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 521 through 537 Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.730A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 589 through 596 removed outlier: 4.287A pdb=" N ARG B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.528A pdb=" N GLU B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 removed outlier: 3.591A pdb=" N ALA B 630 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 4.096A pdb=" N TYR B 635 " --> pdb=" O HIS B 631 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 705 Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.628A pdb=" N LEU B 710 " --> pdb=" O ARG B 706 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 712 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 743 removed outlier: 3.993A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 752 through 763 Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 781 through 791 Processing helix chain 'C' and resid 169 through 174 removed outlier: 4.022A pdb=" N GLN C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 174' Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.549A pdb=" N GLU C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 204 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.725A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 280 removed outlier: 3.757A pdb=" N PHE C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 removed outlier: 3.757A pdb=" N VAL C 293 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 314 Proline residue: C 310 - end of helix removed outlier: 3.772A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.514A pdb=" N ARG C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 371 removed outlier: 3.674A pdb=" N TYR C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 Processing helix chain 'C' and resid 396 through 415 Processing helix chain 'C' and resid 480 through 493 Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.503A pdb=" N GLU C 513 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 537 removed outlier: 3.533A pdb=" N VAL C 525 " --> pdb=" O GLN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 572 removed outlier: 3.879A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.219A pdb=" N SER C 592 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 617 removed outlier: 3.684A pdb=" N GLU C 612 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 630 Processing helix chain 'C' and resid 631 through 644 removed outlier: 4.344A pdb=" N TYR C 635 " --> pdb=" O HIS C 631 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.620A pdb=" N LEU C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 713 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 743 Processing helix chain 'C' and resid 744 through 746 No H-bonds generated for 'chain 'C' and resid 744 through 746' Processing helix chain 'C' and resid 752 through 762 Processing helix chain 'C' and resid 774 through 781 Processing helix chain 'C' and resid 781 through 791 removed outlier: 3.743A pdb=" N PHE C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.862A pdb=" N GLU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.957A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.797A pdb=" N LYS D 243 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 263 through 280 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.703A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Proline residue: D 310 - end of helix removed outlier: 3.878A pdb=" N ARG D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 removed outlier: 4.016A pdb=" N ILE D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 371 removed outlier: 4.774A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.638A pdb=" N MET D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 415 removed outlier: 4.020A pdb=" N MET D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 493 Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 509 through 515 Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 558 through 571 removed outlier: 3.539A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.719A pdb=" N ALA D 576 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 585 No H-bonds generated for 'chain 'D' and resid 583 through 585' Processing helix chain 'D' and resid 587 through 590 Processing helix chain 'D' and resid 591 through 596 removed outlier: 4.222A pdb=" N PHE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 627 through 630 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 634 through 642 removed outlier: 3.937A pdb=" N LEU D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL D 641 " --> pdb=" O SER D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 705 Processing helix chain 'D' and resid 706 through 711 removed outlier: 3.567A pdb=" N LEU D 710 " --> pdb=" O ARG D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 744 removed outlier: 4.004A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 744 " --> pdb=" O GLY D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 781 through 791 Processing helix chain 'E' and resid 169 through 174 removed outlier: 3.946A pdb=" N PHE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 193 through 204 Processing helix chain 'E' and resid 221 through 236 removed outlier: 4.213A pdb=" N VAL E 226 " --> pdb=" O LYS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 263 through 280 Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.592A pdb=" N VAL E 293 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 314 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.639A pdb=" N ARG E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 361 Processing helix chain 'E' and resid 362 through 371 removed outlier: 4.081A pdb=" N TYR E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 390 removed outlier: 3.963A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 415 removed outlier: 3.874A pdb=" N LEU E 402 " --> pdb=" O LYS E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 493 removed outlier: 3.682A pdb=" N ILE E 484 " --> pdb=" O ASP E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 509 removed outlier: 3.852A pdb=" N ARG E 509 " --> pdb=" O THR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 558 through 572 removed outlier: 3.651A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.576A pdb=" N ALA E 576 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.904A pdb=" N PHE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 617 Processing helix chain 'E' and resid 627 through 630 Processing helix chain 'E' and resid 631 through 644 removed outlier: 3.995A pdb=" N TYR E 635 " --> pdb=" O HIS E 631 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 636 " --> pdb=" O GLN E 632 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 641 " --> pdb=" O SER E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 705 Processing helix chain 'E' and resid 706 through 712 Processing helix chain 'E' and resid 723 through 743 Processing helix chain 'E' and resid 744 through 746 No H-bonds generated for 'chain 'E' and resid 744 through 746' Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 770 through 781 removed outlier: 3.687A pdb=" N ILE E 781 " --> pdb=" O ILE E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 791 removed outlier: 3.764A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 No H-bonds generated for 'chain 'F' and resid 171 through 174' Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.532A pdb=" N GLU F 184 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 223 through 236 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 264 through 280 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.009A pdb=" N LEU F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 314 removed outlier: 3.722A pdb=" N LYS F 309 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Proline residue: F 310 - end of helix Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 351 through 371 removed outlier: 4.580A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 390 Processing helix chain 'F' and resid 396 through 415 removed outlier: 3.998A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 493 Processing helix chain 'F' and resid 502 through 508 removed outlier: 3.839A pdb=" N ARG F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 518 removed outlier: 3.926A pdb=" N GLU F 513 " --> pdb=" O ARG F 509 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG F 517 " --> pdb=" O GLU F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 removed outlier: 3.729A pdb=" N ALA F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 571 removed outlier: 3.534A pdb=" N PHE F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 592 Processing helix chain 'F' and resid 610 through 617 removed outlier: 3.615A pdb=" N LYS F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 630 removed outlier: 3.612A pdb=" N ALA F 630 " --> pdb=" O ILE F 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 627 through 630' Processing helix chain 'F' and resid 631 through 645 Processing helix chain 'F' and resid 688 through 704 Processing helix chain 'F' and resid 706 through 712 removed outlier: 3.790A pdb=" N LEU F 710 " --> pdb=" O ARG F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 745 removed outlier: 4.174A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 770 through 781 removed outlier: 3.629A pdb=" N ARG F 774 " --> pdb=" O ALA F 770 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 792 removed outlier: 3.624A pdb=" N LEU F 790 " --> pdb=" O SER F 786 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 251 removed outlier: 8.607A pdb=" N ILE A 320 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 284 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ALA A 322 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ILE A 286 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 323 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 214 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A 213 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 374 removed outlier: 7.115A pdb=" N SER A 373 " --> pdb=" O VAL A 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 581 removed outlier: 3.701A pdb=" N ILE A 580 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 625 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 665 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLY A 547 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE A 664 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A 549 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 548 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE A 717 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A 550 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 3.852A pdb=" N LEU A 647 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 655 " --> pdb=" O LEU A 647 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 4.610A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 322 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.871A pdb=" N SER B 373 " --> pdb=" O VAL B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 578 through 581 removed outlier: 6.074A pdb=" N VAL B 622 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 665 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 624 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 548 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE B 717 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE B 550 " --> pdb=" O ILE B 717 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB1, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.785A pdb=" N ASP B 805 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 817 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 175 through 177 removed outlier: 5.043A pdb=" N ASP C 287 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 322 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 213 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 347 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 215 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 372 through 374 removed outlier: 6.859A pdb=" N SER C 373 " --> pdb=" O VAL C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 578 through 581 removed outlier: 5.950A pdb=" N GLY C 547 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE C 664 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE C 549 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER C 666 " --> pdb=" O PHE C 549 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE C 551 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER C 548 " --> pdb=" O ASP C 715 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE C 717 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 550 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 3.718A pdb=" N LEU C 647 " --> pdb=" O VAL C 655 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 748 through 751 removed outlier: 6.353A pdb=" N ALA C 748 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL C 802 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 750 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N VAL C 804 " --> pdb=" O VAL C 750 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 805 " --> pdb=" O VAL C 817 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 817 " --> pdb=" O ASP C 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.627A pdb=" N GLY D 216 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 373 through 374 removed outlier: 6.689A pdb=" N SER D 373 " --> pdb=" O VAL D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 578 through 581 Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 3.575A pdb=" N LEU D 647 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 748 through 751 removed outlier: 3.759A pdb=" N VAL D 817 " --> pdb=" O ASP D 805 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.553A pdb=" N GLN E 246 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE E 285 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR E 248 " --> pdb=" O PHE E 285 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP E 287 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU E 250 " --> pdb=" O ASP E 287 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA E 322 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN E 211 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 345 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 373 through 374 removed outlier: 7.064A pdb=" N SER E 373 " --> pdb=" O VAL E 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 578 through 581 removed outlier: 6.814A pdb=" N ILE E 578 " --> pdb=" O LEU E 623 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP E 625 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE E 580 " --> pdb=" O ASP E 625 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 547 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER E 548 " --> pdb=" O ASP E 715 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 717 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE E 550 " --> pdb=" O ILE E 717 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 749 through 751 removed outlier: 3.555A pdb=" N ASP E 805 " --> pdb=" O VAL E 817 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 817 " --> pdb=" O ASP E 805 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 175 through 177 removed outlier: 5.833A pdb=" N GLN F 246 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE F 285 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR F 248 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP F 287 " --> pdb=" O TYR F 248 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N LEU F 250 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE F 282 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ILE F 320 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU F 284 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA F 322 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE F 286 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F 216 " --> pdb=" O THR F 323 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN F 211 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL F 345 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL F 213 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 347 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE F 215 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 373 through 374 removed outlier: 7.264A pdb=" N SER F 373 " --> pdb=" O VAL F 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 578 through 581 removed outlier: 6.578A pdb=" N ILE F 578 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP F 625 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE F 580 " --> pdb=" O ASP F 625 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL F 622 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 663 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY F 547 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE F 664 " --> pdb=" O GLY F 547 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE F 549 " --> pdb=" O PHE F 664 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER F 666 " --> pdb=" O PHE F 549 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE F 551 " --> pdb=" O SER F 666 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER F 548 " --> pdb=" O ASP F 715 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE F 717 " --> pdb=" O SER F 548 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE F 550 " --> pdb=" O ILE F 717 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 749 through 750 removed outlier: 3.778A pdb=" N ASP F 805 " --> pdb=" O VAL F 817 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 817 " --> pdb=" O ASP F 805 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3861 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: 9.70 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7740 1.33 - 1.46: 4469 1.46 - 1.58: 15146 1.58 - 1.70: 31 1.70 - 1.82: 132 Bond restraints: 27518 Sorted by residual: bond pdb=" C GLY A 553 " pdb=" N PRO A 554 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.42e+00 bond pdb=" CB PRO F 218 " pdb=" CG PRO F 218 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" C PRO A 554 " pdb=" O PRO A 554 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.18e-02 7.18e+03 3.18e+00 bond pdb=" CA ASP B 815 " pdb=" C ASP B 815 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.66e-02 3.63e+03 2.18e+00 bond pdb=" C ARG B 544 " pdb=" N PRO B 545 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.21e-02 6.83e+03 2.17e+00 ... (remaining 27513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 36507 2.79 - 5.57: 533 5.57 - 8.36: 68 8.36 - 11.14: 11 11.14 - 13.93: 2 Bond angle restraints: 37121 Sorted by residual: angle pdb=" N VAL D 557 " pdb=" CA VAL D 557 " pdb=" C VAL D 557 " ideal model delta sigma weight residual 112.17 105.11 7.06 9.50e-01 1.11e+00 5.53e+01 angle pdb=" CA PRO F 218 " pdb=" N PRO F 218 " pdb=" CD PRO F 218 " ideal model delta sigma weight residual 112.00 104.10 7.90 1.40e+00 5.10e-01 3.18e+01 angle pdb=" CB MET B 415 " pdb=" CG MET B 415 " pdb=" SD MET B 415 " ideal model delta sigma weight residual 112.70 126.63 -13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" N GLY C 769 " pdb=" CA GLY C 769 " pdb=" C GLY C 769 " ideal model delta sigma weight residual 110.29 104.48 5.81 1.28e+00 6.10e-01 2.06e+01 angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 113.53 109.09 4.44 9.80e-01 1.04e+00 2.05e+01 ... (remaining 37116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 16209 30.75 - 61.51: 573 61.51 - 92.26: 43 92.26 - 123.01: 9 123.01 - 153.76: 6 Dihedral angle restraints: 16840 sinusoidal: 7096 harmonic: 9744 Sorted by residual: dihedral pdb=" O2A ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PA ADP D 902 " pdb=" PB ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 93.77 -153.76 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" O1B ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PB ADP D 902 " pdb=" PA ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 80.48 -140.48 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 79.49 -139.48 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 16837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3624 0.068 - 0.136: 580 0.136 - 0.205: 24 0.205 - 0.273: 3 0.273 - 0.341: 2 Chirality restraints: 4233 Sorted by residual: chirality pdb=" CB VAL B 256 " pdb=" CA VAL B 256 " pdb=" CG1 VAL B 256 " pdb=" CG2 VAL B 256 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B 716 " pdb=" CA ILE B 716 " pdb=" CG1 ILE B 716 " pdb=" CG2 ILE B 716 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE C 716 " pdb=" CA ILE C 716 " pdb=" CG1 ILE C 716 " pdb=" CG2 ILE C 716 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4230 not shown) Planarity restraints: 4813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 217 " 0.096 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO F 218 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO F 218 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO F 218 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 597 " -0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO E 598 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO E 598 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 598 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 771 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO E 772 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 772 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 772 " -0.041 5.00e-02 4.00e+02 ... (remaining 4810 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1962 2.74 - 3.28: 27789 3.28 - 3.82: 45303 3.82 - 4.36: 53508 4.36 - 4.90: 90943 Nonbonded interactions: 219505 Sorted by model distance: nonbonded pdb=" O ILE C 627 " pdb=" OH TYR C 635 " model vdw 2.196 3.040 nonbonded pdb=" OE2 GLU A 628 " pdb=" OG SER A 666 " model vdw 2.242 3.040 nonbonded pdb=" O LEU D 733 " pdb=" OG SER D 736 " model vdw 2.252 3.040 nonbonded pdb=" O LEU A 733 " pdb=" OG SER A 736 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR D 500 " pdb=" OE1 GLU D 503 " model vdw 2.266 3.040 ... (remaining 219500 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 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 594 or resid 609 through 668 or resid 691 through 808 or resid 815 through 8 \ 21 or resid 901)) selection = (chain 'B' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'C' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'D' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'E' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 821 or resid 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 821 or resid 901)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.220 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.110 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.004 0.108 27518 Z= 0.174 Angle : 0.834 13.925 37121 Z= 0.428 Chirality : 0.048 0.341 4233 Planarity : 0.006 0.140 4813 Dihedral : 15.490 153.765 10538 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3341 helix: -0.17 (0.12), residues: 1781 sheet: -0.35 (0.25), residues: 400 loop : -0.03 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 807 HIS 0.012 0.001 HIS B 631 PHE 0.025 0.002 PHE F 394 TYR 0.032 0.002 TYR A 389 ARG 0.019 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.16509 ( 1320) hydrogen bonds : angle 6.81113 ( 3861) covalent geometry : bond 0.00385 (27518) covalent geometry : angle 0.83356 (37121) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 653 ARG cc_start: 0.6700 (mtt90) cc_final: 0.5772 (tpt170) REVERT: A 690 TYR cc_start: 0.7134 (p90) cc_final: 0.6855 (m-80) REVERT: A 727 ILE cc_start: 0.6169 (mt) cc_final: 0.5767 (mt) REVERT: A 747 MET cc_start: 0.5193 (mmp) cc_final: 0.4948 (mmm) REVERT: B 325 LEU cc_start: 0.7696 (mt) cc_final: 0.7191 (mp) REVERT: B 587 ASP cc_start: 0.6259 (m-30) cc_final: 0.5472 (p0) REVERT: B 747 MET cc_start: 0.6789 (mtp) cc_final: 0.6570 (mtp) REVERT: C 638 LEU cc_start: 0.8836 (mt) cc_final: 0.8589 (mp) REVERT: D 815 ASP cc_start: 0.6748 (p0) cc_final: 0.5929 (p0) REVERT: E 510 MET cc_start: 0.6444 (ttp) cc_final: 0.6077 (ttp) REVERT: E 730 MET cc_start: 0.7815 (mmm) cc_final: 0.7583 (mmm) REVERT: F 323 THR cc_start: 0.7035 (m) cc_final: 0.6804 (m) REVERT: F 571 PHE cc_start: 0.6059 (m-80) cc_final: 0.5572 (m-80) REVERT: F 573 ASP cc_start: 0.5473 (p0) cc_final: 0.5220 (p0) REVERT: F 587 ASP cc_start: 0.5962 (m-30) cc_final: 0.5537 (t0) REVERT: F 634 ILE cc_start: 0.7688 (mm) cc_final: 0.7420 (mm) REVERT: F 693 MET cc_start: 0.5982 (mmm) cc_final: 0.5763 (ptm) outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.3777 time to fit residues: 255.9864 Evaluate side-chains 317 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 306 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 343 GLN ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN D 659 ASN D 806 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.152547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.117418 restraints weight = 56586.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.117792 restraints weight = 36628.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.118848 restraints weight = 23288.862| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27518 Z= 0.171 Angle : 0.660 8.455 37121 Z= 0.319 Chirality : 0.044 0.220 4233 Planarity : 0.005 0.077 4813 Dihedral : 9.052 163.885 3826 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.20 % Allowed : 9.38 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3341 helix: 0.43 (0.12), residues: 1806 sheet: -0.46 (0.25), residues: 420 loop : 0.24 (0.20), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 807 HIS 0.007 0.001 HIS A 290 PHE 0.028 0.002 PHE C 791 TYR 0.015 0.002 TYR A 635 ARG 0.008 0.001 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 1320) hydrogen bonds : angle 5.19998 ( 3861) covalent geometry : bond 0.00394 (27518) covalent geometry : angle 0.65966 (37121) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 352 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 325 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7503 (mt) REVERT: B 501 GLU cc_start: 0.8360 (mp0) cc_final: 0.7790 (pm20) REVERT: B 633 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5709 (mt-10) REVERT: B 701 LEU cc_start: 0.8415 (pp) cc_final: 0.7939 (tt) REVERT: B 747 MET cc_start: 0.6569 (mtp) cc_final: 0.6284 (mtp) REVERT: C 494 ILE cc_start: 0.7970 (mm) cc_final: 0.7646 (mm) REVERT: C 588 ARG cc_start: 0.6699 (mmp-170) cc_final: 0.5909 (mmm-85) REVERT: D 815 ASP cc_start: 0.7251 (p0) cc_final: 0.6725 (p0) REVERT: E 183 MET cc_start: 0.8955 (mpp) cc_final: 0.7912 (mpp) REVERT: E 510 MET cc_start: 0.6709 (ttp) cc_final: 0.6329 (ttp) REVERT: E 656 ASP cc_start: 0.8338 (p0) cc_final: 0.8080 (p0) REVERT: F 571 PHE cc_start: 0.6077 (m-80) cc_final: 0.5524 (m-80) REVERT: F 573 ASP cc_start: 0.5576 (p0) cc_final: 0.5235 (p0) REVERT: F 587 ASP cc_start: 0.5794 (m-30) cc_final: 0.5537 (p0) REVERT: F 634 ILE cc_start: 0.7721 (mm) cc_final: 0.7503 (mm) REVERT: F 693 MET cc_start: 0.6300 (mmm) cc_final: 0.6032 (ptt) outliers start: 34 outliers final: 18 residues processed: 366 average time/residue: 0.3940 time to fit residues: 231.7138 Evaluate side-chains 323 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain F residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 87 optimal weight: 3.9990 chunk 293 optimal weight: 0.0470 chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 227 optimal weight: 0.0270 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 631 HIS ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 GLN E 343 GLN F 667 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.154064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.119186 restraints weight = 56221.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.120086 restraints weight = 33654.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.121205 restraints weight = 22376.888| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27518 Z= 0.109 Angle : 0.600 7.872 37121 Z= 0.285 Chirality : 0.043 0.207 4233 Planarity : 0.004 0.068 4813 Dihedral : 8.623 165.445 3826 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.30 % Allowed : 12.16 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3341 helix: 0.68 (0.12), residues: 1811 sheet: -0.51 (0.25), residues: 395 loop : 0.39 (0.20), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 PHE 0.020 0.001 PHE D 589 TYR 0.012 0.001 TYR D 604 ARG 0.005 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 1320) hydrogen bonds : angle 4.88223 ( 3861) covalent geometry : bond 0.00244 (27518) covalent geometry : angle 0.60045 (37121) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 333 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5727 (mp) cc_final: 0.5171 (tt) REVERT: A 747 MET cc_start: 0.5071 (mmm) cc_final: 0.4835 (mmm) REVERT: B 325 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7476 (mt) REVERT: B 410 MET cc_start: 0.7730 (mmm) cc_final: 0.7524 (mmm) REVERT: B 501 GLU cc_start: 0.8221 (mp0) cc_final: 0.7745 (pm20) REVERT: B 639 LEU cc_start: 0.8122 (mt) cc_final: 0.7512 (mt) REVERT: B 701 LEU cc_start: 0.8354 (pp) cc_final: 0.7932 (tt) REVERT: B 747 MET cc_start: 0.6636 (mtp) cc_final: 0.6342 (mtp) REVERT: C 494 ILE cc_start: 0.7945 (mm) cc_final: 0.7669 (mm) REVERT: C 588 ARG cc_start: 0.6505 (mmp-170) cc_final: 0.5825 (mmm-85) REVERT: D 201 MET cc_start: 0.8614 (mmm) cc_final: 0.8362 (mmm) REVERT: D 815 ASP cc_start: 0.7224 (p0) cc_final: 0.6603 (p0) REVERT: E 183 MET cc_start: 0.8872 (mpp) cc_final: 0.7906 (mpp) REVERT: E 510 MET cc_start: 0.6827 (ttp) cc_final: 0.6472 (ttp) REVERT: E 656 ASP cc_start: 0.8314 (p0) cc_final: 0.8096 (p0) REVERT: E 696 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7452 (mmtm) REVERT: F 571 PHE cc_start: 0.6073 (m-80) cc_final: 0.5531 (m-80) REVERT: F 573 ASP cc_start: 0.5375 (p0) cc_final: 0.5027 (p0) REVERT: F 693 MET cc_start: 0.6206 (mmm) cc_final: 0.5997 (ptt) outliers start: 37 outliers final: 19 residues processed: 355 average time/residue: 0.3657 time to fit residues: 212.8432 Evaluate side-chains 321 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 300 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 710 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 199 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 148 optimal weight: 0.0980 chunk 99 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 326 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 chunk 312 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN C 586 HIS ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.153248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.118226 restraints weight = 56725.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.118605 restraints weight = 35977.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.119936 restraints weight = 23845.385| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27518 Z= 0.122 Angle : 0.605 8.338 37121 Z= 0.285 Chirality : 0.043 0.288 4233 Planarity : 0.004 0.065 4813 Dihedral : 8.300 165.062 3826 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.69 % Allowed : 13.57 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3341 helix: 0.82 (0.12), residues: 1807 sheet: -0.53 (0.24), residues: 408 loop : 0.44 (0.20), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 PHE 0.024 0.001 PHE D 589 TYR 0.010 0.001 TYR F 328 ARG 0.005 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 1320) hydrogen bonds : angle 4.74617 ( 3861) covalent geometry : bond 0.00281 (27518) covalent geometry : angle 0.60454 (37121) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 330 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5717 (mp) cc_final: 0.5067 (tt) REVERT: B 379 MET cc_start: 0.8028 (mtp) cc_final: 0.7779 (mtp) REVERT: B 501 GLU cc_start: 0.8292 (mp0) cc_final: 0.7803 (pm20) REVERT: B 701 LEU cc_start: 0.8435 (pp) cc_final: 0.7959 (tt) REVERT: B 747 MET cc_start: 0.6528 (mtp) cc_final: 0.6258 (mtp) REVERT: C 494 ILE cc_start: 0.7948 (mm) cc_final: 0.7685 (mm) REVERT: C 588 ARG cc_start: 0.6647 (mmp-170) cc_final: 0.5983 (mmm-85) REVERT: D 201 MET cc_start: 0.8626 (mmm) cc_final: 0.8384 (mmm) REVERT: D 282 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7650 (mp) REVERT: D 815 ASP cc_start: 0.7337 (p0) cc_final: 0.6715 (p0) REVERT: E 187 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7887 (mp) REVERT: E 510 MET cc_start: 0.7026 (ttp) cc_final: 0.6625 (ttp) REVERT: E 656 ASP cc_start: 0.8341 (p0) cc_final: 0.8137 (p0) REVERT: E 696 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7341 (mmtm) REVERT: E 703 LYS cc_start: 0.9299 (mptt) cc_final: 0.9028 (mmtm) REVERT: F 571 PHE cc_start: 0.6136 (m-80) cc_final: 0.5641 (m-80) REVERT: F 573 ASP cc_start: 0.5557 (p0) cc_final: 0.5162 (p0) REVERT: F 617 LYS cc_start: 0.7110 (tppt) cc_final: 0.6373 (mmtm) REVERT: F 693 MET cc_start: 0.6213 (mmm) cc_final: 0.5970 (ptt) outliers start: 48 outliers final: 21 residues processed: 360 average time/residue: 0.3670 time to fit residues: 213.8629 Evaluate side-chains 334 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 274 optimal weight: 0.0570 chunk 218 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 282 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 HIS ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.153025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.118114 restraints weight = 56384.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.118328 restraints weight = 33359.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.119713 restraints weight = 26616.268| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 27518 Z= 0.118 Angle : 0.601 8.860 37121 Z= 0.283 Chirality : 0.042 0.220 4233 Planarity : 0.004 0.065 4813 Dihedral : 8.035 163.461 3826 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.07 % Allowed : 14.73 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3341 helix: 0.92 (0.12), residues: 1791 sheet: -0.52 (0.24), residues: 422 loop : 0.46 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 PHE 0.025 0.001 PHE D 589 TYR 0.009 0.001 TYR B 328 ARG 0.005 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 1320) hydrogen bonds : angle 4.65868 ( 3861) covalent geometry : bond 0.00273 (27518) covalent geometry : angle 0.60051 (37121) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 334 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5854 (mp) cc_final: 0.5263 (tt) REVERT: A 655 VAL cc_start: 0.5992 (OUTLIER) cc_final: 0.5657 (t) REVERT: B 379 MET cc_start: 0.8157 (mtp) cc_final: 0.7898 (mtp) REVERT: B 501 GLU cc_start: 0.8185 (mp0) cc_final: 0.7748 (pm20) REVERT: B 627 ILE cc_start: 0.8919 (tt) cc_final: 0.8549 (tp) REVERT: B 701 LEU cc_start: 0.8391 (pp) cc_final: 0.7930 (tt) REVERT: B 747 MET cc_start: 0.6570 (mtp) cc_final: 0.6304 (mtp) REVERT: C 494 ILE cc_start: 0.7989 (mm) cc_final: 0.7723 (mm) REVERT: C 588 ARG cc_start: 0.6739 (mmp-170) cc_final: 0.6068 (mmm-85) REVERT: D 201 MET cc_start: 0.8584 (mmm) cc_final: 0.8351 (mmm) REVERT: D 815 ASP cc_start: 0.7323 (p0) cc_final: 0.6758 (p0) REVERT: E 656 ASP cc_start: 0.8369 (p0) cc_final: 0.8160 (p0) REVERT: E 696 LYS cc_start: 0.7761 (tmtt) cc_final: 0.7321 (mmtm) REVERT: E 703 LYS cc_start: 0.9315 (mptt) cc_final: 0.9065 (mmtm) REVERT: F 571 PHE cc_start: 0.5872 (m-80) cc_final: 0.5321 (m-80) REVERT: F 573 ASP cc_start: 0.5184 (p0) cc_final: 0.4836 (p0) REVERT: F 617 LYS cc_start: 0.7063 (tppt) cc_final: 0.6317 (mmtm) REVERT: F 693 MET cc_start: 0.6215 (mmm) cc_final: 0.6012 (ptt) REVERT: F 730 MET cc_start: 0.6715 (mmt) cc_final: 0.6430 (mtt) REVERT: F 747 MET cc_start: 0.7606 (mmp) cc_final: 0.7330 (mmt) outliers start: 59 outliers final: 33 residues processed: 372 average time/residue: 0.3633 time to fit residues: 221.1202 Evaluate side-chains 347 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 643 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 741 GLN Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 710 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 91 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 273 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 313 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN C 586 HIS ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS F 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.155162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.121502 restraints weight = 56534.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.121115 restraints weight = 35711.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.122011 restraints weight = 24785.275| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27518 Z= 0.145 Angle : 0.624 10.250 37121 Z= 0.294 Chirality : 0.043 0.274 4233 Planarity : 0.004 0.064 4813 Dihedral : 7.953 163.949 3826 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 16.03 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3341 helix: 0.89 (0.12), residues: 1802 sheet: -0.47 (0.25), residues: 404 loop : 0.41 (0.20), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 491 HIS 0.008 0.001 HIS A 290 PHE 0.027 0.001 PHE D 589 TYR 0.012 0.001 TYR A 635 ARG 0.008 0.000 ARG E 341 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 1320) hydrogen bonds : angle 4.68495 ( 3861) covalent geometry : bond 0.00337 (27518) covalent geometry : angle 0.62356 (37121) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5873 (mp) cc_final: 0.5514 (tt) REVERT: A 655 VAL cc_start: 0.5975 (OUTLIER) cc_final: 0.5473 (t) REVERT: B 410 MET cc_start: 0.7868 (mmm) cc_final: 0.7648 (mmm) REVERT: B 501 GLU cc_start: 0.8165 (mp0) cc_final: 0.7727 (pm20) REVERT: B 627 ILE cc_start: 0.8941 (tt) cc_final: 0.8554 (tp) REVERT: B 701 LEU cc_start: 0.8346 (pp) cc_final: 0.7866 (tt) REVERT: B 747 MET cc_start: 0.6660 (mtp) cc_final: 0.6396 (mtp) REVERT: C 494 ILE cc_start: 0.7944 (mm) cc_final: 0.7612 (mm) REVERT: C 588 ARG cc_start: 0.6761 (mmp-170) cc_final: 0.6053 (mmm-85) REVERT: D 282 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7678 (mp) REVERT: D 690 TYR cc_start: 0.5153 (t80) cc_final: 0.4784 (t80) REVERT: D 815 ASP cc_start: 0.7312 (p0) cc_final: 0.6757 (p0) REVERT: E 183 MET cc_start: 0.9012 (mpp) cc_final: 0.8142 (mpp) REVERT: E 696 LYS cc_start: 0.7774 (tmtt) cc_final: 0.7317 (mmtm) REVERT: E 703 LYS cc_start: 0.9309 (mptt) cc_final: 0.9054 (mmtm) REVERT: F 571 PHE cc_start: 0.5855 (m-80) cc_final: 0.5279 (m-80) REVERT: F 573 ASP cc_start: 0.5131 (p0) cc_final: 0.4772 (p0) REVERT: F 617 LYS cc_start: 0.7120 (tppt) cc_final: 0.6361 (mmtm) REVERT: F 662 LEU cc_start: 0.8094 (mm) cc_final: 0.7833 (mm) outliers start: 55 outliers final: 32 residues processed: 353 average time/residue: 0.4802 time to fit residues: 277.3682 Evaluate side-chains 338 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 6.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 MET Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 732 ASP Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 710 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 171 optimal weight: 0.6980 chunk 264 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 232 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 199 optimal weight: 0.0050 chunk 226 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 148 optimal weight: 0.0980 chunk 240 optimal weight: 0.6980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN D 806 ASN F 640 GLN F 720 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.157735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123866 restraints weight = 56037.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.124548 restraints weight = 34724.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.125590 restraints weight = 21122.432| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27518 Z= 0.104 Angle : 0.610 9.423 37121 Z= 0.286 Chirality : 0.043 0.295 4233 Planarity : 0.004 0.064 4813 Dihedral : 7.634 158.995 3826 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.51 % Allowed : 17.22 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3341 helix: 1.02 (0.12), residues: 1799 sheet: -0.42 (0.25), residues: 410 loop : 0.48 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 PHE 0.030 0.001 PHE D 589 TYR 0.010 0.001 TYR B 635 ARG 0.005 0.000 ARG E 341 Details of bonding type rmsd hydrogen bonds : bond 0.02828 ( 1320) hydrogen bonds : angle 4.56872 ( 3861) covalent geometry : bond 0.00234 (27518) covalent geometry : angle 0.61033 (37121) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5830 (mp) cc_final: 0.5319 (tt) REVERT: B 379 MET cc_start: 0.8134 (mtp) cc_final: 0.7930 (mtp) REVERT: B 501 GLU cc_start: 0.8128 (mp0) cc_final: 0.7706 (pm20) REVERT: B 627 ILE cc_start: 0.8898 (tt) cc_final: 0.8512 (tp) REVERT: B 701 LEU cc_start: 0.8298 (pp) cc_final: 0.7895 (tt) REVERT: B 747 MET cc_start: 0.6663 (mtp) cc_final: 0.6392 (mtp) REVERT: C 494 ILE cc_start: 0.7899 (mm) cc_final: 0.7662 (mm) REVERT: C 588 ARG cc_start: 0.6664 (mmp-170) cc_final: 0.6007 (mmm-85) REVERT: D 282 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7641 (mp) REVERT: D 815 ASP cc_start: 0.7299 (p0) cc_final: 0.6476 (p0) REVERT: E 261 TYR cc_start: 0.7825 (m-80) cc_final: 0.7521 (m-80) REVERT: E 696 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7253 (mmtm) REVERT: E 703 LYS cc_start: 0.9315 (mptt) cc_final: 0.9046 (mmtm) REVERT: F 561 GLU cc_start: 0.5093 (mt-10) cc_final: 0.4829 (mp0) REVERT: F 571 PHE cc_start: 0.5802 (m-80) cc_final: 0.5248 (m-80) REVERT: F 573 ASP cc_start: 0.5117 (p0) cc_final: 0.4758 (p0) REVERT: F 617 LYS cc_start: 0.7108 (tppt) cc_final: 0.6352 (mmtm) REVERT: F 662 LEU cc_start: 0.8101 (mm) cc_final: 0.7745 (mt) REVERT: F 730 MET cc_start: 0.6881 (mtt) cc_final: 0.6647 (mtt) REVERT: F 747 MET cc_start: 0.7391 (mmp) cc_final: 0.7070 (mmt) outliers start: 43 outliers final: 29 residues processed: 353 average time/residue: 0.3581 time to fit residues: 207.0376 Evaluate side-chains 335 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 305 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 232 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 325 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 ASN C 586 HIS D 632 GLN F 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.148338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.114515 restraints weight = 57053.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113939 restraints weight = 35613.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115031 restraints weight = 27177.275| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27518 Z= 0.227 Angle : 0.709 9.202 37121 Z= 0.341 Chirality : 0.046 0.227 4233 Planarity : 0.005 0.063 4813 Dihedral : 7.949 164.428 3826 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.76 % Allowed : 17.82 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3341 helix: 0.73 (0.12), residues: 1809 sheet: -0.65 (0.24), residues: 416 loop : 0.33 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 491 HIS 0.013 0.001 HIS D 290 PHE 0.023 0.002 PHE D 589 TYR 0.015 0.002 TYR B 328 ARG 0.005 0.001 ARG C 646 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 1320) hydrogen bonds : angle 4.83297 ( 3861) covalent geometry : bond 0.00530 (27518) covalent geometry : angle 0.70914 (37121) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 319 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.8482 (mmp) cc_final: 0.8257 (mmt) REVERT: A 653 ARG cc_start: 0.7425 (mtt90) cc_final: 0.5925 (tpt170) REVERT: B 501 GLU cc_start: 0.8149 (mp0) cc_final: 0.7704 (pm20) REVERT: B 627 ILE cc_start: 0.8821 (tt) cc_final: 0.8446 (tp) REVERT: B 634 ILE cc_start: 0.7972 (mm) cc_final: 0.7695 (tp) REVERT: B 701 LEU cc_start: 0.8352 (pp) cc_final: 0.7877 (tt) REVERT: B 747 MET cc_start: 0.6861 (mtp) cc_final: 0.6611 (mtp) REVERT: C 588 ARG cc_start: 0.6865 (mmp-170) cc_final: 0.6559 (mmp-170) REVERT: C 714 ASP cc_start: 0.7905 (t70) cc_final: 0.7671 (t0) REVERT: D 282 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7800 (mp) REVERT: D 815 ASP cc_start: 0.7237 (p0) cc_final: 0.6735 (p0) REVERT: E 183 MET cc_start: 0.8986 (mpp) cc_final: 0.8044 (mpp) REVERT: E 184 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8106 (mt-10) REVERT: E 329 ARG cc_start: 0.7752 (mtm110) cc_final: 0.6922 (mmm160) REVERT: F 571 PHE cc_start: 0.5760 (m-80) cc_final: 0.5227 (m-80) REVERT: F 573 ASP cc_start: 0.5021 (p0) cc_final: 0.4638 (p0) REVERT: F 617 LYS cc_start: 0.7049 (tppt) cc_final: 0.6175 (mmtm) REVERT: F 662 LEU cc_start: 0.8108 (mm) cc_final: 0.7804 (mt) REVERT: F 747 MET cc_start: 0.7320 (mmp) cc_final: 0.7079 (mmt) outliers start: 50 outliers final: 36 residues processed: 352 average time/residue: 0.3392 time to fit residues: 196.4669 Evaluate side-chains 343 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 604 TYR Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 72 optimal weight: 0.4980 chunk 249 optimal weight: 0.9980 chunk 334 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 253 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 270 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.152289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.118101 restraints weight = 56611.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.117671 restraints weight = 35362.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.119093 restraints weight = 23599.433| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27518 Z= 0.126 Angle : 0.645 9.665 37121 Z= 0.306 Chirality : 0.044 0.282 4233 Planarity : 0.004 0.061 4813 Dihedral : 7.653 164.586 3826 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.48 % Allowed : 18.35 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3341 helix: 0.91 (0.12), residues: 1804 sheet: -0.53 (0.25), residues: 403 loop : 0.42 (0.21), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 807 HIS 0.008 0.001 HIS D 290 PHE 0.030 0.001 PHE D 589 TYR 0.010 0.001 TYR B 328 ARG 0.008 0.000 ARG E 314 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 1320) hydrogen bonds : angle 4.67735 ( 3861) covalent geometry : bond 0.00292 (27518) covalent geometry : angle 0.64508 (37121) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 326 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5941 (mp) cc_final: 0.5365 (tt) REVERT: A 653 ARG cc_start: 0.7390 (mtt90) cc_final: 0.7169 (mtt90) REVERT: B 501 GLU cc_start: 0.8186 (mp0) cc_final: 0.7725 (pm20) REVERT: B 627 ILE cc_start: 0.8856 (tt) cc_final: 0.8465 (tp) REVERT: B 634 ILE cc_start: 0.7890 (mm) cc_final: 0.7608 (tp) REVERT: B 701 LEU cc_start: 0.8389 (pp) cc_final: 0.7978 (tt) REVERT: B 747 MET cc_start: 0.6449 (mtp) cc_final: 0.6213 (mtp) REVERT: C 668 LEU cc_start: 0.8439 (tp) cc_final: 0.8180 (tp) REVERT: D 282 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7765 (mp) REVERT: D 771 ARG cc_start: 0.8510 (mtt90) cc_final: 0.7446 (mtm110) REVERT: D 815 ASP cc_start: 0.7342 (p0) cc_final: 0.6785 (p0) REVERT: E 183 MET cc_start: 0.8999 (mpp) cc_final: 0.8043 (mpp) REVERT: E 329 ARG cc_start: 0.7716 (mtm110) cc_final: 0.6892 (mmm160) REVERT: E 415 MET cc_start: 0.3030 (mmt) cc_final: 0.2637 (mpp) REVERT: E 703 LYS cc_start: 0.9282 (mptt) cc_final: 0.8975 (mmtm) REVERT: F 571 PHE cc_start: 0.5801 (m-80) cc_final: 0.5294 (m-80) REVERT: F 573 ASP cc_start: 0.5085 (p0) cc_final: 0.4725 (p0) REVERT: F 617 LYS cc_start: 0.7085 (tppt) cc_final: 0.6273 (mmtm) REVERT: F 662 LEU cc_start: 0.8189 (mm) cc_final: 0.7854 (mt) outliers start: 42 outliers final: 31 residues processed: 351 average time/residue: 0.3654 time to fit residues: 208.7708 Evaluate side-chains 340 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 164 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 225 optimal weight: 0.0000 chunk 104 optimal weight: 3.9990 chunk 329 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 212 optimal weight: 0.0970 chunk 306 optimal weight: 6.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.154715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.122059 restraints weight = 55920.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.120477 restraints weight = 37635.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121334 restraints weight = 27493.674| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27518 Z= 0.124 Angle : 0.657 9.966 37121 Z= 0.311 Chirality : 0.044 0.277 4233 Planarity : 0.004 0.063 4813 Dihedral : 7.479 162.632 3826 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.34 % Allowed : 18.84 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3341 helix: 0.94 (0.12), residues: 1818 sheet: -0.50 (0.25), residues: 410 loop : 0.39 (0.21), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 807 HIS 0.011 0.001 HIS D 290 PHE 0.032 0.001 PHE C 791 TYR 0.016 0.001 TYR E 248 ARG 0.008 0.000 ARG E 314 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 1320) hydrogen bonds : angle 4.65627 ( 3861) covalent geometry : bond 0.00288 (27518) covalent geometry : angle 0.65715 (37121) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.5901 (mp) cc_final: 0.5169 (tt) REVERT: A 693 MET cc_start: 0.2932 (tpt) cc_final: 0.2567 (mtm) REVERT: B 501 GLU cc_start: 0.8169 (mp0) cc_final: 0.7728 (pm20) REVERT: B 627 ILE cc_start: 0.8821 (tt) cc_final: 0.8449 (tp) REVERT: B 701 LEU cc_start: 0.8406 (pp) cc_final: 0.7984 (tt) REVERT: B 747 MET cc_start: 0.6499 (mtp) cc_final: 0.6292 (mtp) REVERT: C 668 LEU cc_start: 0.8461 (tp) cc_final: 0.8212 (tp) REVERT: D 282 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7776 (mp) REVERT: D 771 ARG cc_start: 0.8458 (mtt90) cc_final: 0.7473 (mtm110) REVERT: D 815 ASP cc_start: 0.7345 (p0) cc_final: 0.6802 (p0) REVERT: E 183 MET cc_start: 0.9042 (mpp) cc_final: 0.8064 (mpp) REVERT: E 329 ARG cc_start: 0.7790 (mtm110) cc_final: 0.6849 (mmm160) REVERT: E 415 MET cc_start: 0.3066 (mmt) cc_final: 0.2723 (mpp) REVERT: E 640 GLN cc_start: 0.8479 (pm20) cc_final: 0.8245 (pm20) REVERT: E 703 LYS cc_start: 0.9360 (mptt) cc_final: 0.9063 (mmtm) REVERT: F 571 PHE cc_start: 0.5820 (m-80) cc_final: 0.5315 (m-80) REVERT: F 573 ASP cc_start: 0.5091 (p0) cc_final: 0.4725 (p0) REVERT: F 617 LYS cc_start: 0.7008 (tppt) cc_final: 0.6180 (mmtm) REVERT: F 662 LEU cc_start: 0.8132 (mm) cc_final: 0.7846 (mt) outliers start: 38 outliers final: 33 residues processed: 342 average time/residue: 0.3741 time to fit residues: 210.2494 Evaluate side-chains 342 residues out of total 2845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 720 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 320 optimal weight: 0.0770 chunk 83 optimal weight: 0.0980 chunk 227 optimal weight: 0.0060 chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 205 optimal weight: 0.4980 chunk 135 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 271 optimal weight: 0.8980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.154256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.120136 restraints weight = 56261.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120373 restraints weight = 35451.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.121051 restraints weight = 22211.099| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 27518 Z= 0.108 Angle : 0.654 17.999 37121 Z= 0.308 Chirality : 0.043 0.272 4233 Planarity : 0.004 0.062 4813 Dihedral : 7.177 158.960 3826 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.30 % Allowed : 19.26 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3341 helix: 1.02 (0.12), residues: 1815 sheet: -0.36 (0.25), residues: 420 loop : 0.40 (0.21), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 807 HIS 0.008 0.001 HIS A 290 PHE 0.031 0.001 PHE D 589 TYR 0.016 0.001 TYR B 635 ARG 0.008 0.000 ARG E 314 Details of bonding type rmsd hydrogen bonds : bond 0.02820 ( 1320) hydrogen bonds : angle 4.58584 ( 3861) covalent geometry : bond 0.00243 (27518) covalent geometry : angle 0.65365 (37121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9377.79 seconds wall clock time: 166 minutes 36.70 seconds (9996.70 seconds total)