Starting phenix.real_space_refine on Mon Sep 14 19:08:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.cif" model { file = "/net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ofo_3776/09_2026/5ofo_3776.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 33 5.49 5 S 125 5.16 5 C 20516 2.51 5 N 5965 2.21 5 O 6354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32993 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 1 Chain: "F" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 661} Chain breaks: 1 Chain: "E" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 660} Chain breaks: 1 Chain: "D" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 661} Chain breaks: 1 Chain: "B" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 660} Chain breaks: 1 Chain: "A" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 1 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.41, per 1000 atoms: 0.19 Number of scatterers: 32993 At special positions: 0 Unit cell: (158.92, 165.77, 180.84, 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 125 16.00 P 33 15.00 O 6354 8.00 N 5965 7.00 C 20516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7692 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 28 sheets defined 64.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 316 through 324 Processing helix chain 'C' and resid 326 through 332 Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.515A pdb=" N THR C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 removed outlier: 3.521A pdb=" N ILE C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.575A pdb=" N SER C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 441 through 493 Processing helix chain 'C' and resid 494 through 503 Processing helix chain 'C' and resid 504 through 524 removed outlier: 3.902A pdb=" N GLU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 545 Processing helix chain 'C' and resid 554 through 561 removed outlier: 4.384A pdb=" N LYS C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 570 removed outlier: 3.944A pdb=" N ARG C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 590 Processing helix chain 'C' and resid 610 through 623 Processing helix chain 'C' and resid 640 through 647 removed outlier: 4.340A pdb=" N SER C 644 " --> pdb=" O LYS C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 659 removed outlier: 3.849A pdb=" N GLU C 657 " --> pdb=" O TYR C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 669 removed outlier: 3.845A pdb=" N GLU C 664 " --> pdb=" O GLY C 660 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 removed outlier: 3.921A pdb=" N ALA C 682 " --> pdb=" O VAL C 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 679 through 682' Processing helix chain 'C' and resid 683 through 696 removed outlier: 3.673A pdb=" N PHE C 687 " --> pdb=" O HIS C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 729 removed outlier: 4.935A pdb=" N ARG C 727 " --> pdb=" O ARG C 723 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 729 " --> pdb=" O THR C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 749 removed outlier: 4.488A pdb=" N GLU C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 757 Processing helix chain 'C' and resid 767 through 789 removed outlier: 3.967A pdb=" N ARG C 781 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 782 " --> pdb=" O GLN C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 808 removed outlier: 4.262A pdb=" N TYR C 808 " --> pdb=" O SER C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 835 removed outlier: 4.120A pdb=" N ARG C 819 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 827 " --> pdb=" O GLN C 823 " (cutoff:3.500A) Proline residue: C 828 - end of helix Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.601A pdb=" N ILE F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 225 Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.522A pdb=" N LYS F 233 " --> pdb=" O GLU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 removed outlier: 3.801A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 268 Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.503A pdb=" N ARG F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 361 removed outlier: 4.942A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 381 removed outlier: 3.692A pdb=" N ILE F 370 " --> pdb=" O THR F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 407 Processing helix chain 'F' and resid 409 through 431 Processing helix chain 'F' and resid 437 through 440 removed outlier: 3.691A pdb=" N ARG F 440 " --> pdb=" O SER F 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 437 through 440' Processing helix chain 'F' and resid 441 through 493 Processing helix chain 'F' and resid 494 through 503 Processing helix chain 'F' and resid 504 through 524 removed outlier: 3.541A pdb=" N GLU F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 544 Processing helix chain 'F' and resid 547 through 553 removed outlier: 3.687A pdb=" N MET F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 561 removed outlier: 3.680A pdb=" N LYS F 558 " --> pdb=" O SER F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 570 removed outlier: 3.652A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 590 Processing helix chain 'F' and resid 610 through 623 Processing helix chain 'F' and resid 640 through 647 removed outlier: 4.219A pdb=" N SER F 644 " --> pdb=" O LYS F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 669 Processing helix chain 'F' and resid 678 through 682 Processing helix chain 'F' and resid 683 through 695 Processing helix chain 'F' and resid 718 through 720 No H-bonds generated for 'chain 'F' and resid 718 through 720' Processing helix chain 'F' and resid 721 through 728 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 750 through 757 Processing helix chain 'F' and resid 767 through 788 removed outlier: 4.489A pdb=" N ARG F 781 " --> pdb=" O ILE F 777 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 807 Processing helix chain 'F' and resid 814 through 825 removed outlier: 4.352A pdb=" N LYS F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG F 819 " --> pdb=" O ARG F 815 " (cutoff:3.500A) Processing helix chain 'F' and resid 825 through 834 Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 211 through 225 Processing helix chain 'E' and resid 253 through 268 Processing helix chain 'E' and resid 298 through 306 removed outlier: 4.160A pdb=" N ALA E 302 " --> pdb=" O MET E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 324 Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 342 through 362 removed outlier: 5.386A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 381 Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 409 through 431 removed outlier: 3.906A pdb=" N ARG E 418 " --> pdb=" O ARG E 414 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS E 431 " --> pdb=" O GLN E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 493 Processing helix chain 'E' and resid 494 through 503 Processing helix chain 'E' and resid 505 through 524 Processing helix chain 'E' and resid 533 through 544 Processing helix chain 'E' and resid 548 through 553 Processing helix chain 'E' and resid 554 through 561 removed outlier: 3.644A pdb=" N LYS E 558 " --> pdb=" O SER E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 570 removed outlier: 3.933A pdb=" N ARG E 569 " --> pdb=" O GLU E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 Processing helix chain 'E' and resid 610 through 623 Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 653 through 659 removed outlier: 3.501A pdb=" N GLU E 657 " --> pdb=" O TYR E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 669 removed outlier: 3.641A pdb=" N GLU E 664 " --> pdb=" O GLY E 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 682 removed outlier: 3.572A pdb=" N ALA E 682 " --> pdb=" O VAL E 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 679 through 682' Processing helix chain 'E' and resid 683 through 696 removed outlier: 3.616A pdb=" N PHE E 687 " --> pdb=" O HIS E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 733 through 749 Processing helix chain 'E' and resid 750 through 755 Processing helix chain 'E' and resid 767 through 786 removed outlier: 3.681A pdb=" N ARG E 781 " --> pdb=" O ILE E 777 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 782 " --> pdb=" O GLN E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 790 removed outlier: 3.668A pdb=" N GLY E 790 " --> pdb=" O GLU E 787 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 787 through 790' Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'E' and resid 815 through 825 removed outlier: 4.213A pdb=" N ARG E 819 " --> pdb=" O ARG E 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 836 Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 211 through 225 Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.871A pdb=" N GLU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 361 removed outlier: 5.077A pdb=" N GLU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 380 removed outlier: 3.722A pdb=" N ILE D 370 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 409 through 430 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 441 through 493 Processing helix chain 'D' and resid 494 through 503 Processing helix chain 'D' and resid 504 through 524 removed outlier: 4.127A pdb=" N GLU D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET D 524 " --> pdb=" O GLU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.771A pdb=" N MET D 552 " --> pdb=" O SER D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 561 Processing helix chain 'D' and resid 561 through 570 removed outlier: 3.867A pdb=" N ARG D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 590 removed outlier: 3.536A pdb=" N GLY D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 623 Processing helix chain 'D' and resid 641 through 647 Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.774A pdb=" N GLU D 658 " --> pdb=" O GLY D 655 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 659 " --> pdb=" O TYR D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 659' Processing helix chain 'D' and resid 660 through 669 Processing helix chain 'D' and resid 679 through 682 removed outlier: 3.582A pdb=" N ALA D 682 " --> pdb=" O VAL D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 679 through 682' Processing helix chain 'D' and resid 683 through 695 Processing helix chain 'D' and resid 733 through 749 removed outlier: 4.220A pdb=" N GLU D 744 " --> pdb=" O ASP D 740 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE D 748 " --> pdb=" O GLU D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 756 Processing helix chain 'D' and resid 767 through 790 removed outlier: 3.960A pdb=" N LYS D 780 " --> pdb=" O GLN D 776 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG D 781 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 782 " --> pdb=" O GLN D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 808 removed outlier: 3.628A pdb=" N TYR D 808 " --> pdb=" O SER D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 835 removed outlier: 4.657A pdb=" N ASN D 827 " --> pdb=" O GLN D 823 " (cutoff:3.500A) Proline residue: D 828 - end of helix Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 254 through 270 removed outlier: 4.114A pdb=" N GLY B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 4.596A pdb=" N ALA B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 321 Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.024A pdb=" N ARG B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 5.202A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 409 through 430 removed outlier: 3.954A pdb=" N ALA B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 441 through 493 removed outlier: 3.744A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 removed outlier: 4.036A pdb=" N MET B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 524 Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.612A pdb=" N ARG B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 589 removed outlier: 3.501A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 623 Processing helix chain 'B' and resid 640 through 647 removed outlier: 4.527A pdb=" N SER B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 removed outlier: 4.083A pdb=" N GLU B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 665 " --> pdb=" O TYR B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.820A pdb=" N LYS B 681 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 682 " --> pdb=" O VAL B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 682' Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.906A pdb=" N PHE B 687 " --> pdb=" O HIS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 removed outlier: 3.590A pdb=" N THR B 725 " --> pdb=" O GLY B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 748 Processing helix chain 'B' and resid 750 through 756 Processing helix chain 'B' and resid 767 through 788 removed outlier: 3.962A pdb=" N ARG B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 814 through 835 removed outlier: 4.045A pdb=" N LYS B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) Proline residue: B 828 - end of helix removed outlier: 4.011A pdb=" N GLN B 832 " --> pdb=" O PRO B 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.615A pdb=" N GLU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.990A pdb=" N ALA A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 removed outlier: 3.580A pdb=" N GLU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 342 through 362 removed outlier: 5.676A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.536A pdb=" N ILE A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.912A pdb=" N ARG A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.144A pdb=" N ARG A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 493 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 505 through 524 Processing helix chain 'A' and resid 532 through 545 removed outlier: 3.666A pdb=" N ILE A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 3.582A pdb=" N MET A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 5.324A pdb=" N GLU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.615A pdb=" N GLY A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 Processing helix chain 'A' and resid 625 through 627 No H-bonds generated for 'chain 'A' and resid 625 through 627' Processing helix chain 'A' and resid 641 through 647 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.602A pdb=" N GLU A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.702A pdb=" N LYS A 681 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 682 " --> pdb=" O VAL A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 682' Processing helix chain 'A' and resid 683 through 696 removed outlier: 3.871A pdb=" N PHE A 687 " --> pdb=" O HIS A 683 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.800A pdb=" N SER A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 749 removed outlier: 3.895A pdb=" N ASN A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.912A pdb=" N ILE A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 790 removed outlier: 4.104A pdb=" N ARG A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 782 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 789 " --> pdb=" O ARG A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 825 through 834 Processing sheet with id=AA1, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AA2, first strand: chain 'C' and resid 312 through 315 removed outlier: 8.100A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 629 through 633 removed outlier: 5.867A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 717 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER C 600 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL C 761 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C 602 " --> pdb=" O VAL C 761 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AA5, first strand: chain 'C' and resid 793 through 795 removed outlier: 6.113A pdb=" N HIS C 794 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 165 through 167 removed outlier: 6.299A pdb=" N ARG F 236 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE F 276 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N ASP F 278 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LEU F 240 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.160A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 599 through 600 removed outlier: 5.607A pdb=" N GLY F 599 " --> pdb=" O VAL F 714 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET F 716 " --> pdb=" O GLY F 599 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 602 through 604 removed outlier: 5.476A pdb=" N LEU F 602 " --> pdb=" O VAL F 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 698 through 700 Processing sheet with id=AB2, first strand: chain 'F' and resid 792 through 795 removed outlier: 5.896A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 166 through 167 removed outlier: 6.156A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE E 276 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL E 311 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU E 275 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ALA E 313 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR E 314 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU E 204 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL E 336 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 338 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 205 " --> pdb=" O VAL E 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 630 through 633 removed outlier: 5.557A pdb=" N GLY E 599 " --> pdb=" O VAL E 714 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N MET E 716 " --> pdb=" O GLY E 599 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE E 601 " --> pdb=" O MET E 716 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 698 through 700 Processing sheet with id=AB6, first strand: chain 'E' and resid 792 through 795 removed outlier: 5.526A pdb=" N GLU E 792 " --> pdb=" O ILE E 844 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU E 846 " --> pdb=" O GLU E 792 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL E 848 " --> pdb=" O HIS E 794 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 856 " --> pdb=" O ARG E 845 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 236 through 239 removed outlier: 6.113A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR D 314 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.663A pdb=" N GLN D 364 " --> pdb=" O VAL D 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 630 through 633 removed outlier: 6.479A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE D 601 " --> pdb=" O MET D 716 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 698 through 700 Processing sheet with id=AC2, first strand: chain 'D' and resid 793 through 795 removed outlier: 7.052A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 167 removed outlier: 6.239A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 203 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 364 through 365 removed outlier: 6.619A pdb=" N GLN B 364 " --> pdb=" O VAL B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 629 through 632 removed outlier: 6.443A pdb=" N SER B 672 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE B 715 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 674 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR B 717 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU B 676 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 602 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AC7, first strand: chain 'B' and resid 793 through 794 removed outlier: 6.638A pdb=" N HIS B 794 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL B 848 " --> pdb=" O HIS B 794 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.069A pdb=" N PHE A 276 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL A 311 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A 275 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 629 through 633 removed outlier: 6.018A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER A 672 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE A 715 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY A 599 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N MET A 716 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE A 601 " --> pdb=" O MET A 716 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER A 600 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL A 761 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU A 602 " --> pdb=" O VAL A 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 698 through 700 1846 hydrogen bonds defined for protein. 5493 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: 5.70 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 5968 1.32 - 1.48: 12297 1.48 - 1.63: 14943 1.63 - 1.79: 98 1.79 - 1.95: 129 Bond restraints: 33435 Sorted by residual: bond pdb=" C GLN B 385 " pdb=" N LEU B 386 " ideal model delta sigma weight residual 1.331 1.162 0.169 3.12e-02 1.03e+03 2.92e+01 bond pdb=" O2B AGS D 902 " pdb=" PB AGS D 902 " ideal model delta sigma weight residual 1.531 1.455 0.076 1.60e-02 3.91e+03 2.26e+01 bond pdb=" CA ARG D 183 " pdb=" CB ARG D 183 " ideal model delta sigma weight residual 1.528 1.462 0.065 1.39e-02 5.18e+03 2.19e+01 bond pdb=" C VAL D 760 " pdb=" N VAL D 761 " ideal model delta sigma weight residual 1.329 1.277 0.053 1.17e-02 7.31e+03 2.04e+01 bond pdb=" O2A AGS C 902 " pdb=" PA AGS C 902 " ideal model delta sigma weight residual 1.531 1.461 0.070 1.60e-02 3.91e+03 1.92e+01 ... (remaining 33430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 42978 2.59 - 5.18: 1841 5.18 - 7.76: 215 7.76 - 10.35: 42 10.35 - 12.94: 16 Bond angle restraints: 45092 Sorted by residual: angle pdb=" C VAL B 548 " pdb=" N SER B 549 " pdb=" CA SER B 549 " ideal model delta sigma weight residual 121.70 134.52 -12.82 1.80e+00 3.09e-01 5.07e+01 angle pdb=" C LYS C 747 " pdb=" N ILE C 748 " pdb=" CA ILE C 748 " ideal model delta sigma weight residual 122.77 115.71 7.06 1.05e+00 9.07e-01 4.52e+01 angle pdb=" C VAL C 531 " pdb=" N THR C 532 " pdb=" CA THR C 532 " ideal model delta sigma weight residual 121.70 133.12 -11.42 1.80e+00 3.09e-01 4.03e+01 angle pdb=" C ARG D 440 " pdb=" N LEU D 441 " pdb=" CA LEU D 441 " ideal model delta sigma weight residual 121.54 133.43 -11.89 1.91e+00 2.74e-01 3.88e+01 angle pdb=" C VAL A 246 " pdb=" N ALA A 247 " pdb=" CA ALA A 247 " ideal model delta sigma weight residual 121.70 132.74 -11.04 1.80e+00 3.09e-01 3.76e+01 ... (remaining 45087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 20412 32.04 - 64.08: 309 64.08 - 96.11: 54 96.11 - 128.15: 7 128.15 - 160.19: 5 Dihedral angle restraints: 20787 sinusoidal: 8895 harmonic: 11892 Sorted by residual: dihedral pdb=" CA ASN D 849 " pdb=" C ASN D 849 " pdb=" N GLU D 850 " pdb=" CA GLU D 850 " ideal model delta harmonic sigma weight residual -180.00 -116.47 -63.53 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA TYR A 322 " pdb=" C TYR A 322 " pdb=" N ILE A 323 " pdb=" CA ILE A 323 " ideal model delta harmonic sigma weight residual 180.00 123.76 56.24 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA GLU E 850 " pdb=" C GLU E 850 " pdb=" N ASP E 851 " pdb=" CA ASP E 851 " ideal model delta harmonic sigma weight residual -180.00 -129.93 -50.07 0 5.00e+00 4.00e-02 1.00e+02 ... (remaining 20784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4979 0.144 - 0.288: 110 0.288 - 0.433: 4 0.433 - 0.577: 4 0.577 - 0.721: 3 Chirality restraints: 5100 Sorted by residual: chirality pdb=" PB AGS B 901 " pdb=" O2B AGS B 901 " pdb=" O3A AGS B 901 " pdb=" O3B AGS B 901 " both_signs ideal model delta sigma weight residual True 3.18 2.46 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" PB AGS C 902 " pdb=" O2B AGS C 902 " pdb=" O3A AGS C 902 " pdb=" O3B AGS C 902 " both_signs ideal model delta sigma weight residual True 3.18 2.51 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" PB AGS E 902 " pdb=" O2B AGS E 902 " pdb=" O3A AGS E 902 " pdb=" O3B AGS E 902 " both_signs ideal model delta sigma weight residual True 3.18 2.54 0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 5097 not shown) Planarity restraints: 5885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 850 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C GLU F 850 " 0.103 2.00e-02 2.50e+03 pdb=" O GLU F 850 " -0.038 2.00e-02 2.50e+03 pdb=" N ASP F 851 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 850 " -0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C GLU D 850 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU D 850 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP D 851 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 849 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ASN F 849 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN F 849 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU F 850 " 0.024 2.00e-02 2.50e+03 ... (remaining 5882 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6030 2.76 - 3.29: 33235 3.29 - 3.83: 56573 3.83 - 4.36: 68089 4.36 - 4.90: 107880 Nonbonded interactions: 271807 Sorted by model distance: nonbonded pdb=" OE1 GLU C 658 " pdb=" OH TYR B 656 " model vdw 2.219 3.040 nonbonded pdb=" O SER C 672 " pdb=" OG1 THR C 712 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 625 " pdb=" OE1 GLU B 627 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 612 " pdb=" O2G AGS B 902 " model vdw 2.229 3.040 nonbonded pdb=" O GLN C 735 " pdb=" OG1 THR C 739 " model vdw 2.241 3.040 ... (remaining 271802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 161 through 901) selection = (chain 'C' and resid 161 through 901) selection = (chain 'D' and resid 161 through 901) selection = (chain 'E' and resid 161 through 901) selection = (chain 'F' and resid 161 through 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.360 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 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 : 0.009 0.169 33435 Z= 0.417 Angle : 1.237 12.939 45092 Z= 0.705 Chirality : 0.063 0.721 5100 Planarity : 0.008 0.090 5885 Dihedral : 12.521 160.188 13095 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.40 % Rotamer: Outliers : 0.92 % Allowed : 4.70 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.11), residues: 4092 helix: -2.84 (0.07), residues: 2390 sheet: -1.14 (0.26), residues: 349 loop : -1.79 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG D 815 TYR 0.046 0.004 TYR F 783 PHE 0.035 0.004 PHE A 255 TRP 0.028 0.005 TRP A 543 HIS 0.022 0.003 HIS F 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00875 / 0.42 (33435) covalent geometry : angle 1.23694 / 0.70 (45092) hydrogen bonds : bond 0.14842 / 9.87 ( 1846) hydrogen bonds : angle 10.58142 / 7.50 ( 5493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 648 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 370 ILE cc_start: 0.8825 (pt) cc_final: 0.8587 (mm) REVERT: C 602 LEU cc_start: 0.7779 (tp) cc_final: 0.7372 (tp) REVERT: F 333 PHE cc_start: 0.5632 (m-80) cc_final: 0.5419 (m-80) REVERT: F 422 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8437 (tt) REVERT: F 686 VAL cc_start: 0.6323 (t) cc_final: 0.5885 (p) REVERT: E 618 LEU cc_start: 0.7476 (tp) cc_final: 0.7200 (tp) REVERT: D 308 LEU cc_start: 0.6944 (pt) cc_final: 0.6678 (mt) REVERT: D 401 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8751 (tt) REVERT: D 602 LEU cc_start: 0.7836 (tp) cc_final: 0.7585 (tp) REVERT: D 641 HIS cc_start: 0.5504 (OUTLIER) cc_final: 0.4415 (m-70) REVERT: D 709 PHE cc_start: 0.7076 (m-10) cc_final: 0.6759 (m-10) REVERT: D 797 ASP cc_start: 0.6087 (p0) cc_final: 0.5716 (p0) REVERT: B 584 ILE cc_start: 0.9249 (mt) cc_final: 0.8884 (tp) REVERT: B 602 LEU cc_start: 0.6402 (tp) cc_final: 0.5992 (tp) REVERT: B 632 ILE cc_start: 0.7118 (mt) cc_final: 0.6903 (mm) REVERT: A 333 PHE cc_start: 0.6731 (m-80) cc_final: 0.6513 (m-10) REVERT: A 817 LEU cc_start: 0.6932 (tp) cc_final: 0.6319 (tt) outliers start: 32 outliers final: 5 residues processed: 678 average time/residue: 0.2466 time to fit residues: 253.5355 Evaluate side-chains 317 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 309 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 174 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS C 641 HIS ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN C 755 ASN C 770 HIS C 806 ASN C 822 GLN ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS F 454 GLN ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 574 ASN F 595 ASN F 703 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 620 ASN E 641 HIS E 755 ASN E 778 GLN E 822 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 512 GLN D 595 ASN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN D 719 ASN D 755 ASN D 778 GLN D 806 ASN D 822 GLN B 192 GLN B 195 GLN B 264 ASN B 297 ASN B 683 HIS B 692 GLN B 703 GLN B 737 ASN B 831 GLN B 849 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS A 454 GLN A 488 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN A 778 GLN A 806 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040961 restraints weight = 275408.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042098 restraints weight = 188782.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.042904 restraints weight = 144243.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.043449 restraints weight = 118577.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.043853 restraints weight = 103527.920| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33435 Z= 0.204 Angle : 0.797 15.972 45092 Z= 0.417 Chirality : 0.047 0.263 5100 Planarity : 0.007 0.112 5885 Dihedral : 10.113 153.390 4647 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 0.23 % Allowed : 3.47 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.12), residues: 4092 helix: -1.21 (0.09), residues: 2474 sheet: -1.19 (0.26), residues: 339 loop : -1.52 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 258 TYR 0.023 0.002 TYR F 322 PHE 0.035 0.002 PHE A 601 TRP 0.016 0.003 TRP A 462 HIS 0.007 0.001 HIS B 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (33435) covalent geometry : angle 0.79655 / 0.42 (45092) hydrogen bonds : bond 0.05446 / 3.68 ( 1846) hydrogen bonds : angle 6.63471 / 4.67 ( 5493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 398 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 LEU cc_start: 0.9496 (mt) cc_final: 0.9269 (mt) REVERT: C 479 LEU cc_start: 0.9608 (tt) cc_final: 0.9375 (mt) REVERT: C 562 MET cc_start: 0.9572 (tpp) cc_final: 0.9158 (tpp) REVERT: C 602 LEU cc_start: 0.9208 (tp) cc_final: 0.8967 (tp) REVERT: F 242 MET cc_start: 0.6711 (ppp) cc_final: 0.6208 (tpp) REVERT: F 283 MET cc_start: 0.8395 (mmp) cc_final: 0.8169 (mmm) REVERT: F 552 MET cc_start: 0.9013 (mmp) cc_final: 0.8803 (mmm) REVERT: E 283 MET cc_start: 0.7522 (mmp) cc_final: 0.7104 (mmm) REVERT: E 602 LEU cc_start: 0.9690 (tp) cc_final: 0.9106 (pp) REVERT: E 719 ASN cc_start: 0.8464 (t0) cc_final: 0.7616 (t0) REVERT: E 794 HIS cc_start: 0.8762 (t-170) cc_final: 0.8427 (t-170) REVERT: D 245 LEU cc_start: 0.9295 (mt) cc_final: 0.8853 (mm) REVERT: D 401 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8870 (tt) REVERT: D 602 LEU cc_start: 0.9446 (tp) cc_final: 0.9228 (tp) REVERT: D 629 MET cc_start: 0.8686 (ptp) cc_final: 0.8292 (ptt) REVERT: D 759 GLU cc_start: 0.8165 (mp0) cc_final: 0.7781 (mp0) REVERT: B 308 LEU cc_start: 0.9646 (tp) cc_final: 0.9434 (tp) REVERT: B 314 THR cc_start: 0.9202 (t) cc_final: 0.8769 (t) REVERT: B 566 LEU cc_start: 0.9401 (mt) cc_final: 0.9069 (tt) REVERT: B 661 TYR cc_start: 0.8537 (t80) cc_final: 0.8183 (t80) REVERT: B 742 MET cc_start: 0.9475 (mtm) cc_final: 0.9247 (mtt) REVERT: A 217 GLU cc_start: 0.9457 (OUTLIER) cc_final: 0.9050 (pm20) REVERT: A 242 MET cc_start: 0.0692 (ppp) cc_final: -0.0499 (tpt) REVERT: A 273 VAL cc_start: 0.9579 (p) cc_final: 0.9324 (p) REVERT: A 403 MET cc_start: 0.9434 (ttm) cc_final: 0.9075 (ttm) REVERT: A 487 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8956 (pp20) REVERT: A 829 LEU cc_start: 0.9569 (mp) cc_final: 0.9239 (pp) outliers start: 8 outliers final: 1 residues processed: 405 average time/residue: 0.2167 time to fit residues: 139.9709 Evaluate side-chains 274 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 271 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 54 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 359 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 377 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 309 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 778 GLN F 201 ASN ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 849 ASN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 620 ASN E 683 HIS ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN B 737 ASN B 824 GLN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.055472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040008 restraints weight = 276516.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041063 restraints weight = 191616.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.041810 restraints weight = 147790.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.042343 restraints weight = 122509.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.042649 restraints weight = 107166.405| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33435 Z= 0.191 Angle : 0.724 15.457 45092 Z= 0.377 Chirality : 0.046 0.270 5100 Planarity : 0.006 0.108 5885 Dihedral : 9.655 155.547 4647 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.12), residues: 4092 helix: -0.64 (0.10), residues: 2500 sheet: -1.07 (0.26), residues: 348 loop : -1.38 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG E 222 TYR 0.020 0.002 TYR F 503 PHE 0.025 0.002 PHE A 749 TRP 0.022 0.002 TRP F 543 HIS 0.007 0.001 HIS C 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (33435) covalent geometry : angle 0.72366 / 0.38 (45092) hydrogen bonds : bond 0.04824 / 3.26 ( 1846) hydrogen bonds : angle 5.98894 / 4.23 ( 5493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 324 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 217 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8918 (mt-10) REVERT: C 479 LEU cc_start: 0.9644 (tt) cc_final: 0.9402 (mt) REVERT: C 562 MET cc_start: 0.9472 (tpp) cc_final: 0.9223 (tpt) REVERT: C 737 ASN cc_start: 0.9125 (t0) cc_final: 0.8826 (m110) REVERT: F 298 MET cc_start: 0.7232 (pmm) cc_final: 0.6997 (pmm) REVERT: F 403 MET cc_start: 0.9655 (tpp) cc_final: 0.9384 (tpt) REVERT: F 634 MET cc_start: 0.9283 (mpp) cc_final: 0.9071 (mpp) REVERT: E 283 MET cc_start: 0.6737 (mmp) cc_final: 0.6426 (mmm) REVERT: E 602 LEU cc_start: 0.9720 (tp) cc_final: 0.9089 (pp) REVERT: E 634 MET cc_start: 0.8644 (mpp) cc_final: 0.8264 (mpp) REVERT: E 719 ASN cc_start: 0.8511 (t0) cc_final: 0.7761 (t0) REVERT: E 742 MET cc_start: 0.9231 (mtm) cc_final: 0.8986 (mtp) REVERT: D 242 MET cc_start: 0.8263 (mmm) cc_final: 0.8039 (mmt) REVERT: D 245 LEU cc_start: 0.9289 (mt) cc_final: 0.8852 (mt) REVERT: D 401 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8866 (tt) REVERT: D 602 LEU cc_start: 0.9445 (tp) cc_final: 0.9214 (tp) REVERT: D 629 MET cc_start: 0.8848 (ptp) cc_final: 0.8545 (ptt) REVERT: D 759 GLU cc_start: 0.8311 (mp0) cc_final: 0.7812 (mp0) REVERT: B 280 LEU cc_start: 0.9353 (mt) cc_final: 0.9106 (mt) REVERT: B 308 LEU cc_start: 0.9715 (tp) cc_final: 0.9507 (tp) REVERT: B 562 MET cc_start: 0.9105 (tpp) cc_final: 0.8646 (mmm) REVERT: B 566 LEU cc_start: 0.9330 (mt) cc_final: 0.9095 (tt) REVERT: B 661 TYR cc_start: 0.8481 (t80) cc_final: 0.8227 (t80) REVERT: B 742 MET cc_start: 0.9530 (mtm) cc_final: 0.9305 (mtt) REVERT: A 242 MET cc_start: 0.0310 (ppp) cc_final: -0.0213 (tpt) REVERT: A 403 MET cc_start: 0.9475 (ttm) cc_final: 0.8909 (mtm) REVERT: A 431 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8112 (ttpt) REVERT: A 829 LEU cc_start: 0.9614 (mp) cc_final: 0.9295 (pp) outliers start: 5 outliers final: 1 residues processed: 329 average time/residue: 0.2024 time to fit residues: 110.0199 Evaluate side-chains 241 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 167 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 310 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 368 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN C 822 GLN ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 620 ASN D 195 GLN D 334 GLN D 488 GLN D 512 GLN ** D 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040042 restraints weight = 280419.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041154 restraints weight = 191450.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041921 restraints weight = 146424.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.042387 restraints weight = 120954.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.042815 restraints weight = 106548.308| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 33435 Z= 0.164 Angle : 0.677 16.923 45092 Z= 0.351 Chirality : 0.045 0.222 5100 Planarity : 0.005 0.126 5885 Dihedral : 9.388 158.442 4647 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4092 helix: -0.27 (0.10), residues: 2513 sheet: -1.01 (0.25), residues: 361 loop : -1.20 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 196 TYR 0.021 0.002 TYR C 357 PHE 0.019 0.002 PHE A 749 TRP 0.017 0.002 TRP B 543 HIS 0.005 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (33435) covalent geometry : angle 0.67703 / 0.35 (45092) hydrogen bonds : bond 0.04428 / 3.00 ( 1846) hydrogen bonds : angle 5.61626 / 3.95 ( 5493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 LEU cc_start: 0.9423 (tp) cc_final: 0.9192 (mt) REVERT: C 479 LEU cc_start: 0.9646 (tt) cc_final: 0.9397 (mt) REVERT: C 562 MET cc_start: 0.9450 (tpp) cc_final: 0.9214 (tpp) REVERT: C 602 LEU cc_start: 0.9088 (tp) cc_final: 0.8839 (tp) REVERT: C 737 ASN cc_start: 0.9077 (t0) cc_final: 0.8732 (m-40) REVERT: F 204 LEU cc_start: 0.9759 (mm) cc_final: 0.9434 (mt) REVERT: F 283 MET cc_start: 0.8651 (mmp) cc_final: 0.8431 (mmm) REVERT: F 298 MET cc_start: 0.7384 (pmm) cc_final: 0.7069 (pmm) REVERT: F 329 LEU cc_start: 0.8827 (mt) cc_final: 0.8601 (mt) REVERT: F 333 PHE cc_start: 0.8328 (m-80) cc_final: 0.7936 (m-80) REVERT: F 403 MET cc_start: 0.9599 (tpp) cc_final: 0.9366 (tpt) REVERT: E 298 MET cc_start: 0.9031 (ttm) cc_final: 0.8158 (pmm) REVERT: E 602 LEU cc_start: 0.9704 (tp) cc_final: 0.9295 (mm) REVERT: E 634 MET cc_start: 0.8223 (mpp) cc_final: 0.7983 (mpp) REVERT: E 719 ASN cc_start: 0.7948 (t0) cc_final: 0.7542 (t0) REVERT: E 742 MET cc_start: 0.9262 (mtm) cc_final: 0.9050 (mtp) REVERT: D 245 LEU cc_start: 0.9324 (mt) cc_final: 0.8876 (mt) REVERT: D 317 ASP cc_start: 0.9522 (m-30) cc_final: 0.9077 (t0) REVERT: D 401 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8924 (tt) REVERT: D 629 MET cc_start: 0.9011 (ptp) cc_final: 0.8612 (ptt) REVERT: D 759 GLU cc_start: 0.8324 (mp0) cc_final: 0.7830 (mp0) REVERT: B 308 LEU cc_start: 0.9713 (tp) cc_final: 0.9467 (tp) REVERT: B 562 MET cc_start: 0.8941 (tpp) cc_final: 0.8272 (mmm) REVERT: B 716 MET cc_start: 0.9071 (mmp) cc_final: 0.8871 (mmp) REVERT: B 742 MET cc_start: 0.9565 (mtm) cc_final: 0.9326 (mtt) REVERT: B 750 ARG cc_start: 0.8441 (mpt180) cc_final: 0.8207 (mmt180) REVERT: A 242 MET cc_start: 0.0574 (ppp) cc_final: 0.0260 (tpt) REVERT: A 403 MET cc_start: 0.9474 (ttm) cc_final: 0.8933 (mtm) REVERT: A 431 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8137 (ttpt) REVERT: A 709 PHE cc_start: 0.9242 (m-80) cc_final: 0.9009 (m-10) REVERT: A 829 LEU cc_start: 0.9613 (mp) cc_final: 0.9302 (pp) outliers start: 2 outliers final: 1 residues processed: 328 average time/residue: 0.1944 time to fit residues: 106.1840 Evaluate side-chains 245 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 401 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 312 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN C 794 HIS C 822 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 822 GLN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN E 857 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN B 683 HIS B 688 ASN B 737 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.053644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038474 restraints weight = 288238.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.039542 restraints weight = 195631.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040279 restraints weight = 148905.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.040722 restraints weight = 123066.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041116 restraints weight = 108507.728| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33435 Z= 0.231 Angle : 0.747 16.951 45092 Z= 0.386 Chirality : 0.046 0.285 5100 Planarity : 0.006 0.108 5885 Dihedral : 9.304 156.860 4647 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4092 helix: -0.21 (0.10), residues: 2533 sheet: -1.13 (0.25), residues: 367 loop : -1.15 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 497 TYR 0.019 0.002 TYR F 503 PHE 0.022 0.002 PHE F 621 TRP 0.021 0.002 TRP B 543 HIS 0.007 0.002 HIS D 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (33435) covalent geometry : angle 0.74671 / 0.39 (45092) hydrogen bonds : bond 0.04573 / 3.09 ( 1846) hydrogen bonds : angle 5.60497 / 3.95 ( 5493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 479 LEU cc_start: 0.9619 (tt) cc_final: 0.9381 (mt) REVERT: C 562 MET cc_start: 0.9417 (tpp) cc_final: 0.9216 (tpt) REVERT: C 737 ASN cc_start: 0.9215 (t0) cc_final: 0.8771 (t0) REVERT: F 333 PHE cc_start: 0.8342 (m-80) cc_final: 0.8032 (m-80) REVERT: F 403 MET cc_start: 0.9587 (tpp) cc_final: 0.9327 (tpt) REVERT: F 551 MET cc_start: 0.7969 (pmm) cc_final: 0.7752 (pmm) REVERT: E 298 MET cc_start: 0.9015 (ttm) cc_final: 0.8263 (pmm) REVERT: E 498 MET cc_start: 0.8850 (ptp) cc_final: 0.8606 (ptp) REVERT: E 602 LEU cc_start: 0.9687 (tp) cc_final: 0.9317 (mm) REVERT: E 719 ASN cc_start: 0.8478 (t0) cc_final: 0.8173 (t0) REVERT: E 742 MET cc_start: 0.9237 (mtm) cc_final: 0.8900 (mpp) REVERT: D 245 LEU cc_start: 0.9288 (mt) cc_final: 0.9014 (mt) REVERT: D 317 ASP cc_start: 0.9589 (m-30) cc_final: 0.9115 (t0) REVERT: D 498 MET cc_start: 0.8202 (ppp) cc_final: 0.7847 (ppp) REVERT: D 551 MET cc_start: 0.8928 (mtm) cc_final: 0.8235 (mtt) REVERT: D 629 MET cc_start: 0.9062 (ptp) cc_final: 0.8518 (ptt) REVERT: D 759 GLU cc_start: 0.8217 (mp0) cc_final: 0.7919 (mp0) REVERT: B 308 LEU cc_start: 0.9694 (tp) cc_final: 0.9455 (tp) REVERT: B 403 MET cc_start: 0.9023 (tpp) cc_final: 0.8006 (tmm) REVERT: B 566 LEU cc_start: 0.9318 (mt) cc_final: 0.9117 (tt) REVERT: B 627 GLU cc_start: 0.9238 (mp0) cc_final: 0.8509 (pp20) REVERT: B 742 MET cc_start: 0.9583 (mtm) cc_final: 0.9276 (mtp) REVERT: A 275 LEU cc_start: 0.9546 (tt) cc_final: 0.9063 (mm) REVERT: A 431 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8475 (ttpt) REVERT: A 709 PHE cc_start: 0.9227 (m-80) cc_final: 0.8969 (m-80) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2139 time to fit residues: 105.9129 Evaluate side-chains 227 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 334 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 620 ASN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.055192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.039534 restraints weight = 272322.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.040651 restraints weight = 183663.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041452 restraints weight = 139585.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041978 restraints weight = 114438.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.042359 restraints weight = 100133.906| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33435 Z= 0.141 Angle : 0.671 14.342 45092 Z= 0.344 Chirality : 0.044 0.246 5100 Planarity : 0.005 0.081 5885 Dihedral : 9.108 157.836 4647 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4092 helix: 0.11 (0.10), residues: 2513 sheet: -0.80 (0.25), residues: 368 loop : -1.04 (0.19), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.020 0.002 TYR C 357 PHE 0.023 0.002 PHE A 749 TRP 0.014 0.002 TRP B 543 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (33435) covalent geometry : angle 0.67139 / 0.34 (45092) hydrogen bonds : bond 0.04159 / 2.81 ( 1846) hydrogen bonds : angle 5.34113 / 3.75 ( 5493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ILE cc_start: 0.9596 (mt) cc_final: 0.9252 (tp) REVERT: C 479 LEU cc_start: 0.9620 (tt) cc_final: 0.9395 (mt) REVERT: C 602 LEU cc_start: 0.9027 (tp) cc_final: 0.8674 (tp) REVERT: C 668 ARG cc_start: 0.8330 (mmp80) cc_final: 0.8062 (mmp80) REVERT: C 737 ASN cc_start: 0.9323 (t0) cc_final: 0.8961 (t0) REVERT: F 242 MET cc_start: 0.7705 (pmm) cc_final: 0.7505 (pmm) REVERT: F 283 MET cc_start: 0.8589 (mmp) cc_final: 0.8354 (mmm) REVERT: F 333 PHE cc_start: 0.8310 (m-80) cc_final: 0.7901 (m-80) REVERT: F 403 MET cc_start: 0.9524 (tpp) cc_final: 0.9315 (tpt) REVERT: E 282 THR cc_start: 0.8954 (p) cc_final: 0.8531 (t) REVERT: E 298 MET cc_start: 0.8944 (ttm) cc_final: 0.8262 (pmm) REVERT: E 498 MET cc_start: 0.8794 (ptp) cc_final: 0.8527 (ptp) REVERT: E 562 MET cc_start: 0.9044 (mmp) cc_final: 0.8688 (tpp) REVERT: E 602 LEU cc_start: 0.9701 (tp) cc_final: 0.9335 (mm) REVERT: E 719 ASN cc_start: 0.8738 (t0) cc_final: 0.8530 (t0) REVERT: E 742 MET cc_start: 0.9173 (mtm) cc_final: 0.8871 (mpp) REVERT: D 245 LEU cc_start: 0.9350 (mt) cc_final: 0.8828 (mt) REVERT: D 317 ASP cc_start: 0.9541 (m-30) cc_final: 0.9093 (t0) REVERT: D 498 MET cc_start: 0.7793 (ppp) cc_final: 0.7443 (ppp) REVERT: D 629 MET cc_start: 0.9177 (ptt) cc_final: 0.8599 (ppp) REVERT: D 632 ILE cc_start: 0.8990 (mt) cc_final: 0.8743 (mp) REVERT: B 308 LEU cc_start: 0.9704 (tp) cc_final: 0.9479 (tp) REVERT: B 318 GLU cc_start: 0.8930 (mp0) cc_final: 0.8712 (mp0) REVERT: B 403 MET cc_start: 0.8961 (tpp) cc_final: 0.7963 (tmm) REVERT: B 562 MET cc_start: 0.9415 (tpt) cc_final: 0.8544 (mmm) REVERT: B 627 GLU cc_start: 0.9237 (mp0) cc_final: 0.8635 (pp20) REVERT: B 742 MET cc_start: 0.9553 (mtm) cc_final: 0.9316 (mtt) REVERT: A 310 CYS cc_start: 0.8813 (p) cc_final: 0.8478 (p) REVERT: A 403 MET cc_start: 0.9556 (ttm) cc_final: 0.9030 (ttm) REVERT: A 524 MET cc_start: 0.6895 (tmm) cc_final: 0.6430 (tpt) REVERT: A 552 MET cc_start: 0.8014 (mmm) cc_final: 0.7578 (mmm) REVERT: A 709 PHE cc_start: 0.9183 (m-80) cc_final: 0.8957 (m-80) REVERT: A 829 LEU cc_start: 0.9614 (mp) cc_final: 0.9279 (pp) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.2043 time to fit residues: 106.9428 Evaluate side-chains 234 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 1.9990 chunk 384 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 347 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 620 ASN E 822 GLN ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.054382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.039003 restraints weight = 283590.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040077 restraints weight = 192748.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.040826 restraints weight = 147182.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041353 restraints weight = 121624.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041697 restraints weight = 106545.763| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33435 Z= 0.172 Angle : 0.685 11.128 45092 Z= 0.353 Chirality : 0.045 0.283 5100 Planarity : 0.005 0.066 5885 Dihedral : 9.002 160.479 4647 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4092 helix: 0.17 (0.10), residues: 2537 sheet: -0.74 (0.25), residues: 377 loop : -1.00 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.017 0.002 TYR D 653 PHE 0.021 0.002 PHE F 621 TRP 0.017 0.002 TRP B 543 HIS 0.005 0.001 HIS E 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (33435) covalent geometry : angle 0.68467 / 0.35 (45092) hydrogen bonds : bond 0.04135 / 2.79 ( 1846) hydrogen bonds : angle 5.26892 / 3.70 ( 5493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ILE cc_start: 0.9645 (mt) cc_final: 0.9292 (tp) REVERT: C 318 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 479 LEU cc_start: 0.9634 (tt) cc_final: 0.9400 (mt) REVERT: C 551 MET cc_start: 0.6773 (tpt) cc_final: 0.6567 (mmm) REVERT: C 602 LEU cc_start: 0.8980 (tp) cc_final: 0.8603 (tp) REVERT: C 735 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8838 (tm-30) REVERT: C 737 ASN cc_start: 0.9353 (t160) cc_final: 0.8968 (t0) REVERT: F 242 MET cc_start: 0.7697 (pmm) cc_final: 0.7419 (pmm) REVERT: F 333 PHE cc_start: 0.8408 (m-80) cc_final: 0.8136 (m-80) REVERT: F 403 MET cc_start: 0.9524 (tpp) cc_final: 0.9323 (tpt) REVERT: F 430 MET cc_start: 0.8823 (ptm) cc_final: 0.8612 (ptp) REVERT: E 282 THR cc_start: 0.8999 (p) cc_final: 0.8591 (t) REVERT: E 298 MET cc_start: 0.8979 (ttm) cc_final: 0.8329 (pmm) REVERT: E 498 MET cc_start: 0.8896 (ptp) cc_final: 0.8614 (ptp) REVERT: E 602 LEU cc_start: 0.9664 (tp) cc_final: 0.9281 (mm) REVERT: E 716 MET cc_start: 0.9105 (mmp) cc_final: 0.8870 (mmp) REVERT: E 719 ASN cc_start: 0.8710 (t0) cc_final: 0.8495 (t0) REVERT: E 742 MET cc_start: 0.9157 (mtm) cc_final: 0.8899 (mtp) REVERT: D 245 LEU cc_start: 0.9374 (mt) cc_final: 0.8841 (mt) REVERT: D 317 ASP cc_start: 0.9628 (m-30) cc_final: 0.9139 (t0) REVERT: D 498 MET cc_start: 0.7800 (ppp) cc_final: 0.7455 (ppp) REVERT: D 551 MET cc_start: 0.8598 (mtm) cc_final: 0.8294 (mtt) REVERT: D 629 MET cc_start: 0.9147 (ptt) cc_final: 0.8777 (ppp) REVERT: D 632 ILE cc_start: 0.9038 (mt) cc_final: 0.8825 (mp) REVERT: D 640 LYS cc_start: 0.8203 (pptt) cc_final: 0.7979 (pptt) REVERT: B 260 LYS cc_start: 0.9572 (tptp) cc_final: 0.9253 (pttt) REVERT: B 275 LEU cc_start: 0.9524 (tp) cc_final: 0.9318 (tp) REVERT: B 318 GLU cc_start: 0.9082 (mp0) cc_final: 0.8847 (mp0) REVERT: B 403 MET cc_start: 0.8947 (tpp) cc_final: 0.7978 (tmm) REVERT: B 562 MET cc_start: 0.9396 (tpt) cc_final: 0.8479 (mmm) REVERT: B 627 GLU cc_start: 0.9235 (mp0) cc_final: 0.8785 (pp20) REVERT: B 742 MET cc_start: 0.9547 (mtm) cc_final: 0.9258 (mpp) REVERT: A 242 MET cc_start: 0.4150 (tpt) cc_final: 0.3411 (tpt) REVERT: A 311 VAL cc_start: 0.9760 (t) cc_final: 0.9554 (m) REVERT: A 552 MET cc_start: 0.8419 (mmm) cc_final: 0.8093 (mmm) REVERT: A 709 PHE cc_start: 0.9251 (m-80) cc_final: 0.9004 (m-80) REVERT: A 829 LEU cc_start: 0.9613 (mp) cc_final: 0.9303 (pp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2162 time to fit residues: 105.8512 Evaluate side-chains 235 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 248 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 311 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 365 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 620 ASN E 734 HIS ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN D 827 ASN D 849 ASN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 703 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.053182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038041 restraints weight = 288742.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.039085 restraints weight = 196325.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.039811 restraints weight = 149907.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040319 restraints weight = 124161.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.040646 restraints weight = 108794.322| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 33435 Z= 0.224 Angle : 0.737 11.656 45092 Z= 0.380 Chirality : 0.046 0.285 5100 Planarity : 0.005 0.070 5885 Dihedral : 9.033 160.797 4647 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4092 helix: 0.13 (0.10), residues: 2520 sheet: -1.00 (0.24), residues: 396 loop : -1.08 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 197 TYR 0.040 0.002 TYR C 357 PHE 0.019 0.002 PHE B 687 TRP 0.020 0.002 TRP B 543 HIS 0.006 0.001 HIS D 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (33435) covalent geometry : angle 0.73678 / 0.38 (45092) hydrogen bonds : bond 0.04302 / 2.90 ( 1846) hydrogen bonds : angle 5.41682 / 3.79 ( 5493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ILE cc_start: 0.9698 (mt) cc_final: 0.9335 (tp) REVERT: C 217 GLU cc_start: 0.9468 (mp0) cc_final: 0.9218 (mp0) REVERT: C 318 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8284 (mt-10) REVERT: C 604 LEU cc_start: 0.8850 (tp) cc_final: 0.8590 (tp) REVERT: C 751 PRO cc_start: 0.5766 (Cg_exo) cc_final: 0.5197 (Cg_endo) REVERT: F 242 MET cc_start: 0.7770 (pmm) cc_final: 0.7472 (pmm) REVERT: F 275 LEU cc_start: 0.9636 (tp) cc_final: 0.9396 (pp) REVERT: F 403 MET cc_start: 0.9515 (tpp) cc_final: 0.9287 (tpt) REVERT: F 562 MET cc_start: 0.9538 (ptt) cc_final: 0.9309 (ppp) REVERT: E 282 THR cc_start: 0.9021 (p) cc_final: 0.8771 (p) REVERT: E 298 MET cc_start: 0.8950 (ttm) cc_final: 0.8346 (pmm) REVERT: E 498 MET cc_start: 0.8843 (ptp) cc_final: 0.8555 (ptp) REVERT: E 602 LEU cc_start: 0.9606 (tp) cc_final: 0.9217 (mm) REVERT: E 716 MET cc_start: 0.9044 (mmp) cc_final: 0.8798 (mmp) REVERT: E 794 HIS cc_start: 0.8423 (t-170) cc_final: 0.7966 (t-170) REVERT: D 245 LEU cc_start: 0.9338 (mt) cc_final: 0.8806 (mt) REVERT: D 396 GLU cc_start: 0.9637 (tt0) cc_final: 0.9436 (tt0) REVERT: D 498 MET cc_start: 0.7827 (ppp) cc_final: 0.7452 (ppp) REVERT: B 260 LYS cc_start: 0.9569 (tptp) cc_final: 0.9226 (pttt) REVERT: B 275 LEU cc_start: 0.9310 (tp) cc_final: 0.9102 (tp) REVERT: B 308 LEU cc_start: 0.9746 (tp) cc_final: 0.9507 (mm) REVERT: B 403 MET cc_start: 0.8953 (tpp) cc_final: 0.7990 (tmm) REVERT: B 562 MET cc_start: 0.9426 (tpt) cc_final: 0.8518 (mmm) REVERT: B 627 GLU cc_start: 0.9158 (mp0) cc_final: 0.8604 (pp20) REVERT: B 742 MET cc_start: 0.9549 (mtm) cc_final: 0.9242 (mtp) REVERT: A 403 MET cc_start: 0.9626 (ttm) cc_final: 0.9190 (ttp) REVERT: A 552 MET cc_start: 0.8423 (mmm) cc_final: 0.8118 (mmm) REVERT: A 709 PHE cc_start: 0.9210 (m-80) cc_final: 0.8974 (m-10) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2131 time to fit residues: 102.3867 Evaluate side-chains 220 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 71 optimal weight: 10.0000 chunk 290 optimal weight: 0.0040 chunk 220 optimal weight: 0.3980 chunk 279 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN E 719 ASN E 734 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.054823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.039470 restraints weight = 279164.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.040563 restraints weight = 189064.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041316 restraints weight = 143953.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041839 restraints weight = 119102.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042211 restraints weight = 104255.989| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33435 Z= 0.134 Angle : 0.678 10.821 45092 Z= 0.347 Chirality : 0.045 0.275 5100 Planarity : 0.005 0.083 5885 Dihedral : 8.873 162.540 4647 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4092 helix: 0.34 (0.10), residues: 2535 sheet: -0.55 (0.26), residues: 367 loop : -1.01 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 197 TYR 0.042 0.002 TYR C 357 PHE 0.019 0.002 PHE B 687 TRP 0.019 0.002 TRP F 543 HIS 0.005 0.001 HIS E 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (33435) covalent geometry : angle 0.67845 / 0.35 (45092) hydrogen bonds : bond 0.03977 / 2.68 ( 1846) hydrogen bonds : angle 5.16251 / 3.61 ( 5493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ILE cc_start: 0.9683 (mt) cc_final: 0.9343 (tp) REVERT: C 318 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 604 LEU cc_start: 0.8906 (tp) cc_final: 0.8695 (tp) REVERT: C 622 MET cc_start: 0.8551 (tpt) cc_final: 0.8282 (tpp) REVERT: C 676 LEU cc_start: 0.9263 (mt) cc_final: 0.8910 (mm) REVERT: C 751 PRO cc_start: 0.5272 (Cg_exo) cc_final: 0.4776 (Cg_endo) REVERT: F 403 MET cc_start: 0.9527 (tpp) cc_final: 0.9303 (tpt) REVERT: E 282 THR cc_start: 0.9177 (p) cc_final: 0.8657 (t) REVERT: E 298 MET cc_start: 0.8802 (ttm) cc_final: 0.8224 (pmm) REVERT: E 498 MET cc_start: 0.8776 (ptp) cc_final: 0.8475 (ptp) REVERT: E 602 LEU cc_start: 0.9589 (tp) cc_final: 0.9254 (mm) REVERT: E 757 ILE cc_start: 0.9100 (pt) cc_final: 0.8877 (pt) REVERT: D 245 LEU cc_start: 0.9393 (mt) cc_final: 0.8932 (mt) REVERT: D 396 GLU cc_start: 0.9645 (tt0) cc_final: 0.9325 (tt0) REVERT: D 498 MET cc_start: 0.7834 (ppp) cc_final: 0.7446 (ppp) REVERT: D 629 MET cc_start: 0.9216 (ppp) cc_final: 0.8941 (ppp) REVERT: B 403 MET cc_start: 0.8877 (tpp) cc_final: 0.7889 (tmm) REVERT: B 562 MET cc_start: 0.9401 (tpt) cc_final: 0.8485 (mmm) REVERT: B 627 GLU cc_start: 0.9148 (mp0) cc_final: 0.8777 (pp20) REVERT: B 742 MET cc_start: 0.9520 (mtm) cc_final: 0.9232 (mpp) REVERT: A 403 MET cc_start: 0.9625 (ttm) cc_final: 0.9131 (ttm) REVERT: A 552 MET cc_start: 0.8482 (mmm) cc_final: 0.8190 (mmm) REVERT: A 709 PHE cc_start: 0.9198 (m-80) cc_final: 0.8955 (m-80) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2169 time to fit residues: 112.8141 Evaluate side-chains 241 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 290 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 297 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 0.3980 chunk 241 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.055567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040067 restraints weight = 271970.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041188 restraints weight = 183248.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041956 restraints weight = 139163.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.042492 restraints weight = 114554.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.042875 restraints weight = 99835.782| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33435 Z= 0.125 Angle : 0.662 10.679 45092 Z= 0.337 Chirality : 0.045 0.269 5100 Planarity : 0.005 0.078 5885 Dihedral : 8.715 162.859 4647 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4092 helix: 0.51 (0.10), residues: 2528 sheet: -0.56 (0.25), residues: 386 loop : -0.90 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 379 TYR 0.030 0.001 TYR C 357 PHE 0.027 0.002 PHE A 333 TRP 0.019 0.002 TRP F 543 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (33435) covalent geometry : angle 0.66159 / 0.34 (45092) hydrogen bonds : bond 0.03798 / 2.57 ( 1846) hydrogen bonds : angle 5.02277 / 3.51 ( 5493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ILE cc_start: 0.9674 (mt) cc_final: 0.9385 (tp) REVERT: C 318 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8373 (mt-10) REVERT: C 622 MET cc_start: 0.8582 (tpt) cc_final: 0.8149 (tpp) REVERT: C 627 GLU cc_start: 0.9364 (mp0) cc_final: 0.9139 (pm20) REVERT: C 751 PRO cc_start: 0.5819 (Cg_exo) cc_final: 0.5386 (Cg_endo) REVERT: F 562 MET cc_start: 0.9602 (ptt) cc_final: 0.9353 (ppp) REVERT: E 282 THR cc_start: 0.9193 (p) cc_final: 0.8718 (t) REVERT: E 298 MET cc_start: 0.8864 (ttm) cc_final: 0.8264 (pmm) REVERT: E 498 MET cc_start: 0.8715 (ptp) cc_final: 0.8454 (ptp) REVERT: E 602 LEU cc_start: 0.9633 (tp) cc_final: 0.9250 (mm) REVERT: E 719 ASN cc_start: 0.8646 (t0) cc_final: 0.8329 (t0) REVERT: E 757 ILE cc_start: 0.9068 (pt) cc_final: 0.8800 (pt) REVERT: D 245 LEU cc_start: 0.9469 (mt) cc_final: 0.9207 (mm) REVERT: D 275 LEU cc_start: 0.9582 (tp) cc_final: 0.9210 (tp) REVERT: D 317 ASP cc_start: 0.9560 (m-30) cc_final: 0.8930 (t0) REVERT: D 396 GLU cc_start: 0.9581 (tt0) cc_final: 0.9146 (tt0) REVERT: D 498 MET cc_start: 0.7853 (ppp) cc_final: 0.7487 (ppp) REVERT: D 629 MET cc_start: 0.9311 (ppp) cc_final: 0.8936 (ppp) REVERT: D 644 SER cc_start: 0.9379 (m) cc_final: 0.9076 (p) REVERT: D 709 PHE cc_start: 0.9261 (m-10) cc_final: 0.9050 (m-10) REVERT: B 403 MET cc_start: 0.8793 (tpp) cc_final: 0.7796 (tmm) REVERT: B 562 MET cc_start: 0.9385 (tpt) cc_final: 0.8438 (mmm) REVERT: B 627 GLU cc_start: 0.9142 (mp0) cc_final: 0.8738 (pp20) REVERT: B 742 MET cc_start: 0.9524 (mtm) cc_final: 0.9284 (mtt) REVERT: A 403 MET cc_start: 0.9640 (ttm) cc_final: 0.9150 (ttm) REVERT: A 524 MET cc_start: 0.6365 (tmm) cc_final: 0.6161 (tpp) REVERT: A 552 MET cc_start: 0.8794 (mmm) cc_final: 0.8504 (mmm) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2099 time to fit residues: 110.6322 Evaluate side-chains 241 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 242 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 384 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 253 optimal weight: 0.0670 chunk 220 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 overall best weight: 2.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.054899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039443 restraints weight = 280952.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040524 restraints weight = 190560.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041270 restraints weight = 145764.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041780 restraints weight = 120817.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.042147 restraints weight = 106246.794| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33435 Z= 0.141 Angle : 0.657 10.550 45092 Z= 0.338 Chirality : 0.044 0.266 5100 Planarity : 0.005 0.075 5885 Dihedral : 8.658 162.146 4647 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.13), residues: 4092 helix: 0.60 (0.10), residues: 2529 sheet: -0.56 (0.25), residues: 395 loop : -0.88 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 331 TYR 0.016 0.001 TYR C 357 PHE 0.018 0.002 PHE B 687 TRP 0.015 0.002 TRP F 543 HIS 0.013 0.001 HIS E 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (33435) covalent geometry : angle 0.65682 / 0.34 (45092) hydrogen bonds : bond 0.03758 / 2.54 ( 1846) hydrogen bonds : angle 5.02103 / 3.50 ( 5493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.58 seconds wall clock time: 102 minutes 22.54 seconds (6142.54 seconds total)