Starting phenix.real_space_refine on Fri Mar 6 04:12:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7teb_25844/03_2026/7teb_25844.cif Found real_map, /net/cci-nas-00/data/ceres_data/7teb_25844/03_2026/7teb_25844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7teb_25844/03_2026/7teb_25844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7teb_25844/03_2026/7teb_25844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7teb_25844/03_2026/7teb_25844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7teb_25844/03_2026/7teb_25844.map" } resolution = 4.23 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= 0.054 sd= 0.469 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: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 17990 2.51 5 N 4710 2.21 5 O 5287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28161 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 751} Chain breaks: 4 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6177 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6186 Classifications: {'peptide': 784} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 752} Chain breaks: 4 Chain: "D" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6177 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 5.85, per 1000 atoms: 0.21 Number of scatterers: 28161 At special positions: 0 Unit cell: (146.59, 226.05, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 5287 8.00 N 4710 7.00 C 17990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=1.53 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.05 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=1.81 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.28 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.13 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=1.54 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=1.86 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.05 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=1.80 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.21 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6644 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 41 sheets defined 34.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.646A pdb=" N ASN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.827A pdb=" N SER A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.145A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 4.168A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.727A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 6.442A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 4.126A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.699A pdb=" N ARG A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.341A pdb=" N ARG A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 318 removed outlier: 3.662A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 4.204A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.646A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.722A pdb=" N GLN A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 547' Processing helix chain 'A' and resid 585 through 604 removed outlier: 3.750A pdb=" N PHE A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 636 removed outlier: 3.828A pdb=" N GLY A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 678 removed outlier: 3.541A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 690 removed outlier: 4.089A pdb=" N ASN A 689 " --> pdb=" O THR A 686 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP A 690 " --> pdb=" O GLY A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 690' Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.550A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 removed outlier: 3.525A pdb=" N GLU A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.830A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 5.097A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 791 removed outlier: 4.310A pdb=" N GLN A 791 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.656A pdb=" N ILE A 797 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.591A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 841 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.700A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.552A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.730A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.651A pdb=" N ASN B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 289 through 303 removed outlier: 3.647A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 removed outlier: 4.184A pdb=" N MET B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.581A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.553A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.651A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 521' Processing helix chain 'B' and resid 557 through 567 removed outlier: 4.398A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.794A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.822A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 654 removed outlier: 4.244A pdb=" N VAL B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.794A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.709A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.774A pdb=" N VAL B 776 " --> pdb=" O TRP B 772 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 793 through 796 Processing helix chain 'B' and resid 813 through 817 removed outlier: 4.157A pdb=" N ASP B 816 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 817 " --> pdb=" O ASP B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 813 through 817' Processing helix chain 'B' and resid 818 through 838 removed outlier: 4.033A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.647A pdb=" N ASN C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.830A pdb=" N SER C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 111 removed outlier: 4.145A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 4.126A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 removed outlier: 3.728A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 6.443A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.626A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 removed outlier: 3.700A pdb=" N ARG C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.663A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 4.203A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.646A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.722A pdb=" N GLN C 546 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR C 547 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 547' Processing helix chain 'C' and resid 585 through 604 removed outlier: 3.750A pdb=" N PHE C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 636 removed outlier: 3.828A pdb=" N GLY C 633 " --> pdb=" O TRP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 678 removed outlier: 3.540A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 690 removed outlier: 4.089A pdb=" N ASN C 689 " --> pdb=" O THR C 686 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP C 690 " --> pdb=" O GLY C 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 686 through 690' Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.550A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 removed outlier: 3.525A pdb=" N GLU C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.830A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 5.096A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 791 removed outlier: 4.311A pdb=" N GLN C 791 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 803 removed outlier: 3.655A pdb=" N ILE C 797 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.590A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 846 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.701A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.553A pdb=" N ILE D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.730A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.651A pdb=" N ASN D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.646A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 339 removed outlier: 4.184A pdb=" N MET D 334 " --> pdb=" O TYR D 330 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.582A pdb=" N LYS D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 472 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 removed outlier: 3.551A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.651A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 521' Processing helix chain 'D' and resid 557 through 567 removed outlier: 4.397A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.794A pdb=" N PHE D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 612 removed outlier: 3.823A pdb=" N GLY D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 654 removed outlier: 4.244A pdb=" N VAL D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 696 removed outlier: 3.794A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.710A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.774A pdb=" N VAL D 776 " --> pdb=" O TRP D 772 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 793 through 796 Processing helix chain 'D' and resid 813 through 817 removed outlier: 4.157A pdb=" N ASP D 816 " --> pdb=" O LEU D 813 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D 817 " --> pdb=" O ASP D 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 813 through 817' Processing helix chain 'D' and resid 818 through 838 removed outlier: 4.032A pdb=" N ALA D 828 " --> pdb=" O MET D 824 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 833 " --> pdb=" O MET D 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 217 removed outlier: 6.087A pdb=" N ILE A 163 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A 214 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 216 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 167 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.305A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.734A pdb=" N THR A 423 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 434 Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.609A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 518 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.710A pdb=" N ARG B 67 " --> pdb=" O ILE B 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.604A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 256 through 257 removed outlier: 5.709A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 279 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AB2, first strand: chain 'B' and resid 408 through 410 removed outlier: 6.194A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 420 Processing sheet with id=AB4, first strand: chain 'B' and resid 488 through 490 removed outlier: 4.081A pdb=" N LYS B 488 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 524 through 525 removed outlier: 3.997A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB7, first strand: chain 'B' and resid 534 through 538 removed outlier: 3.557A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 212 through 217 removed outlier: 6.086A pdb=" N ILE C 163 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS C 214 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 216 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 290 through 292 removed outlier: 6.209A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.734A pdb=" N THR C 423 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.868A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 508 through 511 removed outlier: 3.608A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 518 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AC5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.709A pdb=" N ARG D 67 " --> pdb=" O ILE D 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 97 through 100 removed outlier: 6.605A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 256 through 257 removed outlier: 5.709A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 279 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 362 through 363 Processing sheet with id=AC9, first strand: chain 'D' and resid 408 through 410 removed outlier: 6.193A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AD2, first strand: chain 'D' and resid 488 through 490 removed outlier: 4.081A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 524 through 525 removed outlier: 3.998A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD5, first strand: chain 'D' and resid 534 through 538 removed outlier: 3.557A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.618A pdb=" N LYS H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.838A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.838A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.764A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE L 21 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.643A pdb=" N THR L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU M 81 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS M 22 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU M 79 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.826A pdb=" N SER M 35 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA M 97 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET M 93 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.764A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE N 21 " --> pdb=" O PHE N 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.643A pdb=" N THR N 101 " --> pdb=" O TYR N 86 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2349 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: 4.94 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4668 1.32 - 1.46: 11072 1.46 - 1.61: 12735 1.61 - 1.75: 2 1.75 - 1.90: 296 Bond restraints: 28773 Sorted by residual: bond pdb=" C ILE D 108 " pdb=" O ILE D 108 " ideal model delta sigma weight residual 1.232 1.272 -0.041 1.15e-02 7.56e+03 1.24e+01 bond pdb=" C ILE B 108 " pdb=" O ILE B 108 " ideal model delta sigma weight residual 1.232 1.272 -0.040 1.15e-02 7.56e+03 1.24e+01 bond pdb=" CA PHE B 176 " pdb=" CB PHE B 176 " ideal model delta sigma weight residual 1.526 1.578 -0.052 1.59e-02 3.96e+03 1.05e+01 bond pdb=" CA PHE D 176 " pdb=" CB PHE D 176 " ideal model delta sigma weight residual 1.526 1.578 -0.052 1.59e-02 3.96e+03 1.05e+01 bond pdb=" CB CYS A 457 " pdb=" SG CYS A 457 " ideal model delta sigma weight residual 1.808 1.899 -0.091 3.30e-02 9.18e+02 7.64e+00 ... (remaining 28768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 38208 4.37 - 8.73: 638 8.73 - 13.10: 95 13.10 - 17.46: 9 17.46 - 21.83: 4 Bond angle restraints: 38954 Sorted by residual: angle pdb=" CA CYS C 476 " pdb=" CB CYS C 476 " pdb=" SG CYS C 476 " ideal model delta sigma weight residual 114.40 136.23 -21.83 2.30e+00 1.89e-01 9.00e+01 angle pdb=" CA CYS A 476 " pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " ideal model delta sigma weight residual 114.40 136.22 -21.82 2.30e+00 1.89e-01 9.00e+01 angle pdb=" N GLY A 265 " pdb=" CA GLY A 265 " pdb=" C GLY A 265 " ideal model delta sigma weight residual 110.69 98.40 12.29 1.33e+00 5.65e-01 8.54e+01 angle pdb=" N GLY B 377 " pdb=" CA GLY B 377 " pdb=" C GLY B 377 " ideal model delta sigma weight residual 110.66 128.21 -17.55 1.90e+00 2.77e-01 8.54e+01 angle pdb=" N GLY D 377 " pdb=" CA GLY D 377 " pdb=" C GLY D 377 " ideal model delta sigma weight residual 110.66 128.21 -17.55 1.90e+00 2.77e-01 8.53e+01 ... (remaining 38949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.27: 15711 23.27 - 46.54: 1267 46.54 - 69.81: 172 69.81 - 93.08: 37 93.08 - 116.35: 2 Dihedral angle restraints: 17189 sinusoidal: 6845 harmonic: 10344 Sorted by residual: dihedral pdb=" CA GLN D 357 " pdb=" C GLN D 357 " pdb=" N MET D 358 " pdb=" CA MET D 358 " ideal model delta harmonic sigma weight residual 180.00 63.65 116.35 0 5.00e+00 4.00e-02 5.41e+02 dihedral pdb=" CA GLN B 357 " pdb=" C GLN B 357 " pdb=" N MET B 358 " pdb=" CA MET B 358 " ideal model delta harmonic sigma weight residual 180.00 63.67 116.33 0 5.00e+00 4.00e-02 5.41e+02 dihedral pdb=" CA PRO A 403 " pdb=" C PRO A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta harmonic sigma weight residual 180.00 107.33 72.67 0 5.00e+00 4.00e-02 2.11e+02 ... (remaining 17186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3798 0.105 - 0.210: 478 0.210 - 0.315: 50 0.315 - 0.420: 12 0.420 - 0.525: 6 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CB ILE N 83 " pdb=" CA ILE N 83 " pdb=" CG1 ILE N 83 " pdb=" CG2 ILE N 83 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CB ILE L 83 " pdb=" CA ILE L 83 " pdb=" CG1 ILE L 83 " pdb=" CG2 ILE L 83 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" CB ILE D 534 " pdb=" CA ILE D 534 " pdb=" CG1 ILE D 534 " pdb=" CG2 ILE D 534 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 4341 not shown) Planarity restraints: 4947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 83 " -0.033 2.00e-02 2.50e+03 6.60e-02 4.36e+01 pdb=" C THR B 83 " 0.114 2.00e-02 2.50e+03 pdb=" O THR B 83 " -0.042 2.00e-02 2.50e+03 pdb=" N ARG B 84 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 83 " -0.033 2.00e-02 2.50e+03 6.60e-02 4.36e+01 pdb=" C THR D 83 " 0.114 2.00e-02 2.50e+03 pdb=" O THR D 83 " -0.042 2.00e-02 2.50e+03 pdb=" N ARG D 84 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 184 " -0.031 2.00e-02 2.50e+03 6.09e-02 3.70e+01 pdb=" C ASN D 184 " 0.105 2.00e-02 2.50e+03 pdb=" O ASN D 184 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS D 185 " -0.036 2.00e-02 2.50e+03 ... (remaining 4944 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 21 2.08 - 2.78: 6730 2.78 - 3.49: 36786 3.49 - 4.19: 64428 4.19 - 4.90: 106470 Nonbonded interactions: 214435 Sorted by model distance: nonbonded pdb=" O ILE C 29 " pdb=" OG1 THR C 63 " model vdw 1.373 3.040 nonbonded pdb=" O PHE A 137 " pdb=" O LEU A 138 " model vdw 1.437 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR A 122 " model vdw 1.619 3.040 nonbonded pdb=" OG SER C 93 " pdb=" OG1 THR C 122 " model vdw 1.627 3.040 nonbonded pdb=" CG2 VAL A 118 " pdb=" O SER A 136 " model vdw 1.650 3.460 ... (remaining 214430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 27 through 187 or resid 211 through 862)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'H' and resid 2 through 120) selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.440 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.504 28793 Z= 0.448 Angle : 1.477 36.180 38992 Z= 0.838 Chirality : 0.073 0.525 4344 Planarity : 0.009 0.109 4947 Dihedral : 16.520 116.346 10488 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 1.70 % Allowed : 11.65 % Favored : 86.65 % Rotamer: Outliers : 3.86 % Allowed : 11.49 % Favored : 84.65 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 7.35 % Twisted General : 1.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.11), residues: 3528 helix: -3.19 (0.10), residues: 1116 sheet: -2.26 (0.24), residues: 398 loop : -3.30 (0.11), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 375 TYR 0.059 0.003 TYR B 167 PHE 0.083 0.003 PHE D 176 TRP 0.093 0.004 TRP C 402 HIS 0.024 0.003 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00590 (28773) covalent geometry : angle 1.40959 (38954) SS BOND : bond 0.19707 ( 19) SS BOND : angle 14.18009 ( 38) hydrogen bonds : bond 0.19828 ( 810) hydrogen bonds : angle 7.78748 ( 2349) Misc. bond : bond 0.37467 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 256 time to evaluate : 1.004 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: A 136 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7478 (m) REVERT: A 463 THR cc_start: 0.5596 (OUTLIER) cc_final: 0.5375 (p) REVERT: A 586 LEU cc_start: 0.9139 (mp) cc_final: 0.8937 (tt) REVERT: A 598 LEU cc_start: 0.8636 (mt) cc_final: 0.8420 (mt) REVERT: A 723 MET cc_start: 0.6938 (tpt) cc_final: 0.6154 (tpt) REVERT: A 783 MET cc_start: 0.5041 (mtp) cc_final: 0.4836 (mtm) REVERT: A 834 MET cc_start: 0.8006 (tpt) cc_final: 0.7153 (mpp) REVERT: B 54 HIS cc_start: 0.8165 (p-80) cc_final: 0.7688 (p-80) REVERT: B 207 MET cc_start: 0.6494 (mpp) cc_final: 0.5197 (mmm) REVERT: C 411 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5088 (mmt-90) REVERT: C 463 THR cc_start: 0.6370 (OUTLIER) cc_final: 0.6000 (p) REVERT: C 586 LEU cc_start: 0.9245 (mp) cc_final: 0.8920 (tt) REVERT: C 589 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8697 (pp) REVERT: C 723 MET cc_start: 0.6752 (tpt) cc_final: 0.6023 (tpt) REVERT: D 54 HIS cc_start: 0.8240 (p-80) cc_final: 0.7988 (p90) REVERT: D 207 MET cc_start: 0.6491 (mpp) cc_final: 0.4913 (mmm) REVERT: D 386 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.3724 (mmm) REVERT: D 829 MET cc_start: 0.8385 (tmm) cc_final: 0.8164 (tmm) REVERT: H 3 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8419 (mmmt) REVERT: H 34 MET cc_start: 0.5985 (mmm) cc_final: 0.5176 (mmm) REVERT: L 22 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.5048 (t) REVERT: L 28 ASP cc_start: 0.6889 (m-30) cc_final: 0.6178 (p0) REVERT: L 82 ASP cc_start: 0.4291 (p0) cc_final: 0.3621 (p0) REVERT: M 3 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7767 (tptt) REVERT: M 34 MET cc_start: 0.7111 (mmm) cc_final: 0.6751 (mmm) REVERT: M 80 TYR cc_start: 0.7544 (m-80) cc_final: 0.6902 (m-80) REVERT: N 5 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7710 (t) REVERT: N 22 THR cc_start: 0.6465 (OUTLIER) cc_final: 0.6220 (t) REVERT: N 24 LYS cc_start: 0.9162 (mttt) cc_final: 0.8926 (mmmt) REVERT: N 50 TYR cc_start: 0.6699 (m-10) cc_final: 0.6316 (p90) REVERT: N 72 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8066 (m) outliers start: 119 outliers final: 22 residues processed: 362 average time/residue: 0.1781 time to fit residues: 102.1598 Evaluate side-chains 218 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN B 311 HIS B 333 ASN B 357 GLN B 495 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 147 GLN C 508 GLN D 311 HIS D 357 GLN D 495 ASN L 38 HIS L 49 HIS L 55 GLN N 38 HIS N 49 HIS N 55 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.049041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.035737 restraints weight = 362943.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.036400 restraints weight = 224692.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.036719 restraints weight = 162299.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.036973 restraints weight = 135436.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.036973 restraints weight = 119638.638| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28793 Z= 0.181 Angle : 0.821 9.411 38992 Z= 0.438 Chirality : 0.048 0.295 4344 Planarity : 0.006 0.087 4947 Dihedral : 7.859 78.768 3854 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.61 % Favored : 89.82 % Rotamer: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.73 % 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: -3.32 (0.12), residues: 3528 helix: -1.41 (0.13), residues: 1150 sheet: -1.57 (0.24), residues: 437 loop : -2.96 (0.12), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 98 TYR 0.024 0.002 TYR B 252 PHE 0.047 0.002 PHE A 42 TRP 0.035 0.002 TRP C 151 HIS 0.013 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00389 (28773) covalent geometry : angle 0.81735 (38954) SS BOND : bond 0.01690 ( 19) SS BOND : angle 2.60195 ( 38) hydrogen bonds : bond 0.04787 ( 810) hydrogen bonds : angle 5.71769 ( 2349) Misc. bond : bond 0.01056 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 191 time to evaluate : 1.057 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: A 154 MET cc_start: 0.9354 (mtm) cc_final: 0.9120 (mtp) REVERT: A 155 MET cc_start: 0.7265 (ttp) cc_final: 0.6873 (tmm) REVERT: A 375 MET cc_start: 0.8738 (mmp) cc_final: 0.8375 (mpp) REVERT: A 415 MET cc_start: 0.8516 (tpt) cc_final: 0.8296 (mmm) REVERT: A 523 MET cc_start: 0.9223 (ttm) cc_final: 0.8726 (ttm) REVERT: A 662 MET cc_start: 0.9626 (tmm) cc_final: 0.9352 (tmm) REVERT: B 54 HIS cc_start: 0.8672 (p-80) cc_final: 0.8434 (p-80) REVERT: B 73 MET cc_start: 0.8414 (tpp) cc_final: 0.8193 (tpp) REVERT: B 89 MET cc_start: 0.9580 (mmp) cc_final: 0.8794 (tpt) REVERT: B 207 MET cc_start: 0.6934 (mpp) cc_final: 0.6412 (mmm) REVERT: B 386 MET cc_start: 0.4635 (mmp) cc_final: 0.4228 (mmm) REVERT: B 394 MET cc_start: 0.6599 (ptp) cc_final: 0.6295 (pmm) REVERT: B 537 MET cc_start: 0.8847 (tmm) cc_final: 0.8467 (tmm) REVERT: B 561 MET cc_start: 0.9465 (mtm) cc_final: 0.8925 (mtt) REVERT: B 654 MET cc_start: 0.9341 (tmm) cc_final: 0.8998 (tmm) REVERT: B 809 MET cc_start: 0.8179 (pmm) cc_final: 0.7736 (pmm) REVERT: C 154 MET cc_start: 0.9438 (mtm) cc_final: 0.9150 (mtp) REVERT: C 347 MET cc_start: 0.9434 (ptt) cc_final: 0.9157 (ppp) REVERT: C 375 MET cc_start: 0.8410 (mmp) cc_final: 0.8125 (mmm) REVERT: C 523 MET cc_start: 0.9249 (ttm) cc_final: 0.8753 (ttm) REVERT: C 839 MET cc_start: 0.8420 (ppp) cc_final: 0.8161 (ptt) REVERT: D 207 MET cc_start: 0.6999 (mpp) cc_final: 0.5832 (mmm) REVERT: D 386 MET cc_start: 0.5464 (mmm) cc_final: 0.5228 (mmm) REVERT: D 394 MET cc_start: 0.6134 (ptp) cc_final: 0.5812 (pmm) REVERT: D 537 MET cc_start: 0.8756 (tmm) cc_final: 0.8433 (tmm) REVERT: D 829 MET cc_start: 0.9034 (tmm) cc_final: 0.8771 (tmm) REVERT: H 34 MET cc_start: 0.6140 (mmm) cc_final: 0.5389 (mmm) REVERT: M 34 MET cc_start: 0.5512 (mmm) cc_final: 0.5217 (mmm) REVERT: M 83 MET cc_start: 0.3533 (mmp) cc_final: 0.2802 (mmm) outliers start: 5 outliers final: 0 residues processed: 196 average time/residue: 0.1784 time to fit residues: 55.8315 Evaluate side-chains 159 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 173 optimal weight: 0.0970 chunk 166 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 chunk 328 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 726 HIS B 486 HIS ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS N 49 HIS N 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.048639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.035183 restraints weight = 364707.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.035719 restraints weight = 225009.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.036597 restraints weight = 167329.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.036847 restraints weight = 137238.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.037339 restraints weight = 122531.303| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28793 Z= 0.149 Angle : 0.731 9.889 38992 Z= 0.387 Chirality : 0.046 0.251 4344 Planarity : 0.005 0.076 4947 Dihedral : 7.194 69.792 3854 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.64 % Favored : 89.91 % Rotamer: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.67 % 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: -2.56 (0.13), residues: 3528 helix: -0.36 (0.15), residues: 1140 sheet: -1.25 (0.25), residues: 412 loop : -2.75 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 38 TYR 0.018 0.002 TYR D 252 PHE 0.031 0.002 PHE A 137 TRP 0.024 0.002 TRP C 402 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00324 (28773) covalent geometry : angle 0.72802 (38954) SS BOND : bond 0.00267 ( 19) SS BOND : angle 2.08059 ( 38) hydrogen bonds : bond 0.03796 ( 810) hydrogen bonds : angle 5.15443 ( 2349) Misc. bond : bond 0.00929 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.871 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: A 154 MET cc_start: 0.9339 (mtm) cc_final: 0.9078 (mtp) REVERT: A 155 MET cc_start: 0.7484 (ttp) cc_final: 0.6981 (tmm) REVERT: A 375 MET cc_start: 0.8825 (mmp) cc_final: 0.8460 (mpp) REVERT: A 415 MET cc_start: 0.8500 (tpt) cc_final: 0.8216 (mmm) REVERT: A 662 MET cc_start: 0.9596 (tmm) cc_final: 0.9345 (tmm) REVERT: B 73 MET cc_start: 0.8303 (tpp) cc_final: 0.8026 (tpp) REVERT: B 89 MET cc_start: 0.9546 (mmp) cc_final: 0.8911 (tpt) REVERT: B 132 MET cc_start: 0.7172 (tpp) cc_final: 0.6457 (tpp) REVERT: B 142 MET cc_start: 0.6709 (mpp) cc_final: 0.6447 (pmm) REVERT: B 207 MET cc_start: 0.7340 (mpp) cc_final: 0.6666 (mmm) REVERT: B 386 MET cc_start: 0.4482 (mmp) cc_final: 0.3817 (mmm) REVERT: B 394 MET cc_start: 0.6235 (ptp) cc_final: 0.5960 (pmm) REVERT: B 537 MET cc_start: 0.8876 (tmm) cc_final: 0.8520 (tmm) REVERT: B 561 MET cc_start: 0.9441 (mtm) cc_final: 0.8914 (ptp) REVERT: B 654 MET cc_start: 0.9403 (tmm) cc_final: 0.9022 (tmm) REVERT: B 809 MET cc_start: 0.8441 (pmm) cc_final: 0.8039 (pmm) REVERT: C 154 MET cc_start: 0.9509 (mtm) cc_final: 0.9152 (mtp) REVERT: C 155 MET cc_start: 0.6366 (ttt) cc_final: 0.5975 (tmm) REVERT: C 347 MET cc_start: 0.9451 (ptt) cc_final: 0.9147 (ppp) REVERT: C 375 MET cc_start: 0.8379 (mmp) cc_final: 0.8152 (mmm) REVERT: C 662 MET cc_start: 0.9612 (tmm) cc_final: 0.9404 (tmm) REVERT: C 839 MET cc_start: 0.8406 (ppp) cc_final: 0.8154 (ptt) REVERT: D 132 MET cc_start: 0.7139 (tpp) cc_final: 0.6477 (tpp) REVERT: D 207 MET cc_start: 0.7383 (mpp) cc_final: 0.6745 (mmm) REVERT: D 386 MET cc_start: 0.5232 (mmm) cc_final: 0.4915 (mtp) REVERT: D 394 MET cc_start: 0.6002 (ptp) cc_final: 0.5657 (pmm) REVERT: D 537 MET cc_start: 0.8759 (tmm) cc_final: 0.8382 (tmm) REVERT: D 654 MET cc_start: 0.9389 (tmm) cc_final: 0.9177 (tmm) REVERT: D 809 MET cc_start: 0.8507 (pmm) cc_final: 0.7364 (tpt) REVERT: D 818 MET cc_start: 0.9379 (tpt) cc_final: 0.9172 (mmm) REVERT: D 829 MET cc_start: 0.8967 (tmm) cc_final: 0.8738 (tmm) REVERT: H 34 MET cc_start: 0.6510 (mmm) cc_final: 0.5815 (mmp) REVERT: H 83 MET cc_start: 0.5864 (mmp) cc_final: 0.4648 (mtm) REVERT: M 83 MET cc_start: 0.4351 (mmp) cc_final: 0.3421 (mmp) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1759 time to fit residues: 54.4607 Evaluate side-chains 159 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 101 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 348 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN B 711 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS D 218 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS D 711 GLN N 49 HIS N 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.046953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.034125 restraints weight = 370267.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.034258 restraints weight = 239901.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.034681 restraints weight = 184240.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.034945 restraints weight = 151150.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.034945 restraints weight = 133729.946| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28793 Z= 0.191 Angle : 0.735 11.824 38992 Z= 0.387 Chirality : 0.045 0.242 4344 Planarity : 0.005 0.070 4947 Dihedral : 6.935 63.747 3854 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.67 % Favored : 89.99 % Rotamer: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.59 % 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: -2.11 (0.14), residues: 3528 helix: 0.24 (0.15), residues: 1156 sheet: -1.41 (0.25), residues: 400 loop : -2.54 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 124 TYR 0.017 0.002 TYR B 507 PHE 0.025 0.002 PHE M 29 TRP 0.020 0.002 TRP D 796 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00406 (28773) covalent geometry : angle 0.73332 (38954) SS BOND : bond 0.00470 ( 19) SS BOND : angle 1.74383 ( 38) hydrogen bonds : bond 0.03709 ( 810) hydrogen bonds : angle 5.04542 ( 2349) Misc. bond : bond 0.00916 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.110 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: A 154 MET cc_start: 0.9392 (mtm) cc_final: 0.9018 (mtp) REVERT: A 155 MET cc_start: 0.7681 (ttp) cc_final: 0.7058 (tmm) REVERT: A 375 MET cc_start: 0.8985 (mmp) cc_final: 0.8739 (mpp) REVERT: A 523 MET cc_start: 0.8689 (ttm) cc_final: 0.8097 (ttm) REVERT: A 655 MET cc_start: 0.7842 (mmm) cc_final: 0.7642 (mmm) REVERT: A 662 MET cc_start: 0.9606 (tmm) cc_final: 0.9353 (tmm) REVERT: B 142 MET cc_start: 0.7444 (mpp) cc_final: 0.6962 (mpp) REVERT: B 207 MET cc_start: 0.7083 (mpp) cc_final: 0.6593 (mmm) REVERT: B 386 MET cc_start: 0.4973 (mmp) cc_final: 0.3511 (tpp) REVERT: B 537 MET cc_start: 0.8888 (tmm) cc_final: 0.8505 (tmm) REVERT: B 561 MET cc_start: 0.9508 (mtm) cc_final: 0.8980 (mtt) REVERT: B 706 MET cc_start: 0.8895 (tmm) cc_final: 0.8645 (tmm) REVERT: B 809 MET cc_start: 0.8736 (pmm) cc_final: 0.7327 (tpt) REVERT: B 829 MET cc_start: 0.8970 (tmm) cc_final: 0.8723 (tmm) REVERT: C 154 MET cc_start: 0.9509 (mtm) cc_final: 0.9082 (mtp) REVERT: C 155 MET cc_start: 0.6950 (ttt) cc_final: 0.6218 (tmm) REVERT: C 375 MET cc_start: 0.8534 (mmp) cc_final: 0.8303 (mmm) REVERT: C 523 MET cc_start: 0.8764 (ttm) cc_final: 0.8232 (ttm) REVERT: C 662 MET cc_start: 0.9586 (tmm) cc_final: 0.9327 (tmm) REVERT: C 839 MET cc_start: 0.7842 (ppp) cc_final: 0.7504 (ptm) REVERT: D 89 MET cc_start: 0.9484 (ptp) cc_final: 0.9272 (ppp) REVERT: D 142 MET cc_start: 0.7387 (mpp) cc_final: 0.7104 (mpp) REVERT: D 207 MET cc_start: 0.7297 (mpp) cc_final: 0.6881 (mmm) REVERT: D 386 MET cc_start: 0.5689 (mmm) cc_final: 0.5283 (tpp) REVERT: D 537 MET cc_start: 0.8840 (tmm) cc_final: 0.8517 (tmm) REVERT: D 654 MET cc_start: 0.9401 (tmm) cc_final: 0.9162 (tmm) REVERT: D 706 MET cc_start: 0.8913 (tmm) cc_final: 0.8675 (tmm) REVERT: D 809 MET cc_start: 0.8991 (pmm) cc_final: 0.7448 (tpt) REVERT: D 818 MET cc_start: 0.9379 (tpt) cc_final: 0.9143 (mmm) REVERT: D 829 MET cc_start: 0.9059 (tmm) cc_final: 0.8762 (tmm) REVERT: M 34 MET cc_start: 0.6703 (mmt) cc_final: 0.6422 (mmt) REVERT: M 83 MET cc_start: 0.3232 (mmp) cc_final: 0.2160 (mmm) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.1743 time to fit residues: 52.4148 Evaluate side-chains 158 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 247 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 351 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 542 ASN B 218 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 542 ASN C 801 HIS D 159 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.046113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.032794 restraints weight = 373971.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.033495 restraints weight = 237049.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.034004 restraints weight = 177307.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.034195 restraints weight = 151661.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.034345 restraints weight = 138430.686| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28793 Z= 0.205 Angle : 0.748 10.600 38992 Z= 0.395 Chirality : 0.046 0.240 4344 Planarity : 0.005 0.067 4947 Dihedral : 6.883 58.554 3854 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.66 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.56 % 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: -1.90 (0.14), residues: 3528 helix: 0.50 (0.15), residues: 1149 sheet: -1.37 (0.25), residues: 391 loop : -2.44 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 238 TYR 0.018 0.002 TYR D 507 PHE 0.021 0.002 PHE A 137 TRP 0.053 0.002 TRP B 379 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00424 (28773) covalent geometry : angle 0.74480 (38954) SS BOND : bond 0.01292 ( 19) SS BOND : angle 2.25381 ( 38) hydrogen bonds : bond 0.03638 ( 810) hydrogen bonds : angle 5.05522 ( 2349) Misc. bond : bond 0.00829 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.037 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: A 154 MET cc_start: 0.9383 (mtm) cc_final: 0.8968 (mtp) REVERT: A 155 MET cc_start: 0.7696 (ttp) cc_final: 0.7260 (tmm) REVERT: A 375 MET cc_start: 0.9045 (mmp) cc_final: 0.8830 (mpp) REVERT: A 523 MET cc_start: 0.8665 (ttm) cc_final: 0.8067 (ttm) REVERT: B 142 MET cc_start: 0.7655 (mpp) cc_final: 0.7328 (mpp) REVERT: B 207 MET cc_start: 0.7291 (mpp) cc_final: 0.6863 (mmm) REVERT: B 386 MET cc_start: 0.5209 (mmp) cc_final: 0.4235 (tmm) REVERT: B 537 MET cc_start: 0.8982 (tmm) cc_final: 0.8547 (tmm) REVERT: B 561 MET cc_start: 0.9454 (mtm) cc_final: 0.8934 (mtt) REVERT: B 565 MET cc_start: 0.8811 (mmt) cc_final: 0.8500 (tpp) REVERT: B 654 MET cc_start: 0.9427 (tmm) cc_final: 0.9089 (tmm) REVERT: B 706 MET cc_start: 0.8738 (tmm) cc_final: 0.8478 (tmm) REVERT: B 809 MET cc_start: 0.8947 (pmm) cc_final: 0.7449 (tpt) REVERT: B 829 MET cc_start: 0.9017 (tmm) cc_final: 0.8806 (tmm) REVERT: C 154 MET cc_start: 0.9524 (mtm) cc_final: 0.9072 (mtp) REVERT: C 155 MET cc_start: 0.7426 (ttt) cc_final: 0.6638 (tmm) REVERT: C 523 MET cc_start: 0.8689 (ttm) cc_final: 0.8095 (ttm) REVERT: C 839 MET cc_start: 0.7844 (ppp) cc_final: 0.7576 (ptm) REVERT: D 73 MET cc_start: 0.8289 (tpp) cc_final: 0.7760 (tmm) REVERT: D 89 MET cc_start: 0.9617 (ptp) cc_final: 0.9412 (ppp) REVERT: D 207 MET cc_start: 0.7341 (mpp) cc_final: 0.6910 (mmm) REVERT: D 537 MET cc_start: 0.8925 (tmm) cc_final: 0.8514 (tmm) REVERT: D 654 MET cc_start: 0.9450 (tmm) cc_final: 0.9190 (tmm) REVERT: D 706 MET cc_start: 0.8880 (tmm) cc_final: 0.8639 (tmm) REVERT: D 809 MET cc_start: 0.9057 (pmm) cc_final: 0.7439 (tpt) REVERT: D 818 MET cc_start: 0.9306 (tpt) cc_final: 0.8958 (mmm) REVERT: D 829 MET cc_start: 0.8990 (tmm) cc_final: 0.8678 (tmm) REVERT: H 34 MET cc_start: 0.6635 (mmm) cc_final: 0.5974 (mmm) REVERT: M 83 MET cc_start: 0.3406 (mmp) cc_final: 0.2639 (mmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1828 time to fit residues: 54.4767 Evaluate side-chains 164 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 24 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 227 optimal weight: 0.7980 chunk 331 optimal weight: 50.0000 chunk 181 optimal weight: 20.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 217 GLN A 801 HIS B 60 HIS B 357 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 801 HIS D 357 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.044997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031885 restraints weight = 378671.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.032347 restraints weight = 243780.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.032725 restraints weight = 185354.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.032879 restraints weight = 153596.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033428 restraints weight = 136894.709| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28793 Z= 0.246 Angle : 0.794 12.799 38992 Z= 0.417 Chirality : 0.046 0.235 4344 Planarity : 0.005 0.068 4947 Dihedral : 6.997 56.278 3854 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.59 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.53 % 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: -2.00 (0.14), residues: 3528 helix: 0.36 (0.15), residues: 1179 sheet: -1.62 (0.25), residues: 382 loop : -2.46 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 358 TYR 0.024 0.002 TYR D 254 PHE 0.022 0.002 PHE A 137 TRP 0.067 0.003 TRP D 379 HIS 0.009 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00511 (28773) covalent geometry : angle 0.79232 (38954) SS BOND : bond 0.00406 ( 19) SS BOND : angle 1.87817 ( 38) hydrogen bonds : bond 0.03916 ( 810) hydrogen bonds : angle 5.17082 ( 2349) Misc. bond : bond 0.00832 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.060 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: A 154 MET cc_start: 0.9456 (mtm) cc_final: 0.8981 (mtp) REVERT: A 155 MET cc_start: 0.7891 (ttp) cc_final: 0.7371 (tmm) REVERT: A 375 MET cc_start: 0.9121 (mmp) cc_final: 0.8907 (mpp) REVERT: A 523 MET cc_start: 0.8874 (ttm) cc_final: 0.8647 (ttm) REVERT: A 662 MET cc_start: 0.9698 (tmm) cc_final: 0.9397 (tmm) REVERT: A 839 MET cc_start: 0.7547 (ptt) cc_final: 0.7271 (ptt) REVERT: B 142 MET cc_start: 0.7143 (mpp) cc_final: 0.6472 (mpp) REVERT: B 207 MET cc_start: 0.7428 (mpp) cc_final: 0.7135 (mmm) REVERT: B 537 MET cc_start: 0.8918 (tmm) cc_final: 0.8546 (tmm) REVERT: B 561 MET cc_start: 0.9582 (mtm) cc_final: 0.9048 (mtt) REVERT: B 654 MET cc_start: 0.9522 (tmm) cc_final: 0.9206 (tmm) REVERT: B 706 MET cc_start: 0.8950 (tmm) cc_final: 0.8603 (tmm) REVERT: B 809 MET cc_start: 0.8947 (pmm) cc_final: 0.7480 (tpt) REVERT: B 829 MET cc_start: 0.8988 (tmm) cc_final: 0.8738 (tmm) REVERT: C 154 MET cc_start: 0.9593 (mtm) cc_final: 0.9109 (mtp) REVERT: C 155 MET cc_start: 0.7305 (ttt) cc_final: 0.6544 (tmm) REVERT: C 375 MET cc_start: 0.8803 (mmp) cc_final: 0.8525 (mmm) REVERT: C 523 MET cc_start: 0.8787 (ttm) cc_final: 0.8571 (ttm) REVERT: C 662 MET cc_start: 0.9702 (tmm) cc_final: 0.9446 (tmm) REVERT: C 839 MET cc_start: 0.7716 (ppp) cc_final: 0.7506 (ptm) REVERT: D 142 MET cc_start: 0.6818 (mpp) cc_final: 0.5815 (mpp) REVERT: D 207 MET cc_start: 0.7532 (mpp) cc_final: 0.7224 (mmm) REVERT: D 503 MET cc_start: 0.9459 (tpt) cc_final: 0.9209 (tpp) REVERT: D 537 MET cc_start: 0.9053 (tmm) cc_final: 0.8718 (tmm) REVERT: D 561 MET cc_start: 0.9391 (ptp) cc_final: 0.9185 (ptp) REVERT: D 654 MET cc_start: 0.9555 (tmm) cc_final: 0.9301 (tmm) REVERT: D 706 MET cc_start: 0.8912 (tmm) cc_final: 0.8557 (tmm) REVERT: D 809 MET cc_start: 0.8985 (pmm) cc_final: 0.7745 (tpt) REVERT: D 829 MET cc_start: 0.8968 (tmm) cc_final: 0.8654 (tmm) REVERT: H 83 MET cc_start: 0.5730 (mmp) cc_final: 0.4507 (mtm) REVERT: M 34 MET cc_start: 0.6205 (mmt) cc_final: 0.5831 (mmm) REVERT: M 83 MET cc_start: 0.3754 (mmp) cc_final: 0.2920 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1638 time to fit residues: 50.2256 Evaluate side-chains 160 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 5.9990 chunk 78 optimal weight: 0.0030 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.0070 chunk 139 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 322 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 overall best weight: 2.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.046028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3078 r_free = 0.3078 target = 0.032729 restraints weight = 371652.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.033494 restraints weight = 232740.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.033843 restraints weight = 172699.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.033996 restraints weight = 144058.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.034331 restraints weight = 129608.349| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28793 Z= 0.142 Angle : 0.705 9.092 38992 Z= 0.367 Chirality : 0.045 0.241 4344 Planarity : 0.005 0.069 4947 Dihedral : 6.705 57.474 3854 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.06 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.53 % 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: -1.70 (0.14), residues: 3528 helix: 0.66 (0.15), residues: 1177 sheet: -1.39 (0.25), residues: 394 loop : -2.32 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.022 0.002 TYR A 668 PHE 0.032 0.002 PHE A 137 TRP 0.034 0.002 TRP D 379 HIS 0.007 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00310 (28773) covalent geometry : angle 0.70258 (38954) SS BOND : bond 0.00461 ( 19) SS BOND : angle 1.84631 ( 38) hydrogen bonds : bond 0.03465 ( 810) hydrogen bonds : angle 4.90055 ( 2349) Misc. bond : bond 0.00814 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.103 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: A 154 MET cc_start: 0.9431 (mtm) cc_final: 0.8908 (mtp) REVERT: A 155 MET cc_start: 0.8030 (ttp) cc_final: 0.7578 (tmm) REVERT: A 347 MET cc_start: 0.9446 (ptt) cc_final: 0.9223 (ppp) REVERT: A 375 MET cc_start: 0.9108 (mmp) cc_final: 0.8815 (mpp) REVERT: A 415 MET cc_start: 0.8621 (tpt) cc_final: 0.8222 (mmm) REVERT: A 662 MET cc_start: 0.9693 (tmm) cc_final: 0.9369 (tmm) REVERT: A 834 MET cc_start: 0.9428 (tpt) cc_final: 0.9136 (tpp) REVERT: A 839 MET cc_start: 0.7507 (ptt) cc_final: 0.7261 (ptt) REVERT: B 132 MET cc_start: 0.6806 (tpp) cc_final: 0.6562 (tpp) REVERT: B 537 MET cc_start: 0.9006 (tmm) cc_final: 0.8684 (tmm) REVERT: B 561 MET cc_start: 0.9555 (mtm) cc_final: 0.9121 (mtt) REVERT: B 654 MET cc_start: 0.9546 (tmm) cc_final: 0.9229 (tmm) REVERT: B 706 MET cc_start: 0.8967 (tmm) cc_final: 0.8642 (tmm) REVERT: B 809 MET cc_start: 0.9102 (pmm) cc_final: 0.7632 (tpt) REVERT: B 829 MET cc_start: 0.9055 (tmm) cc_final: 0.8829 (tmm) REVERT: C 74 MET cc_start: 0.8407 (mtt) cc_final: 0.7773 (mmt) REVERT: C 154 MET cc_start: 0.9548 (mtm) cc_final: 0.9063 (mtp) REVERT: C 155 MET cc_start: 0.7256 (ttt) cc_final: 0.6537 (tmm) REVERT: C 375 MET cc_start: 0.8578 (mmp) cc_final: 0.8089 (mpp) REVERT: C 436 MET cc_start: 0.8776 (mpp) cc_final: 0.8479 (mpp) REVERT: C 523 MET cc_start: 0.8968 (ttm) cc_final: 0.8736 (ttm) REVERT: D 132 MET cc_start: 0.6867 (tpp) cc_final: 0.6593 (tpp) REVERT: D 142 MET cc_start: 0.6152 (mpp) cc_final: 0.5655 (mpp) REVERT: D 307 MET cc_start: 0.8155 (ptt) cc_final: 0.7931 (ptt) REVERT: D 394 MET cc_start: 0.5934 (pmm) cc_final: 0.5583 (pmm) REVERT: D 503 MET cc_start: 0.9452 (tpt) cc_final: 0.9147 (tpp) REVERT: D 537 MET cc_start: 0.9016 (tmm) cc_final: 0.8647 (tmm) REVERT: D 654 MET cc_start: 0.9531 (tmm) cc_final: 0.9263 (tmm) REVERT: D 706 MET cc_start: 0.8983 (tmm) cc_final: 0.8659 (tmm) REVERT: D 809 MET cc_start: 0.9030 (pmm) cc_final: 0.7850 (tpt) REVERT: D 829 MET cc_start: 0.9039 (tmm) cc_final: 0.8719 (tmm) REVERT: H 83 MET cc_start: 0.5521 (mmp) cc_final: 0.4313 (mtm) REVERT: M 83 MET cc_start: 0.3651 (mmp) cc_final: 0.3007 (mmp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1658 time to fit residues: 50.2146 Evaluate side-chains 160 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 198 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 317 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 73 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.046536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.035764 restraints weight = 371104.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.035340 restraints weight = 237652.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.035825 restraints weight = 164612.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.036110 restraints weight = 123680.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.036182 restraints weight = 111358.119| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28793 Z= 0.122 Angle : 0.687 9.242 38992 Z= 0.357 Chirality : 0.045 0.243 4344 Planarity : 0.005 0.070 4947 Dihedral : 6.485 55.914 3854 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.46 % Favored : 89.37 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.44 % 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: -1.57 (0.14), residues: 3528 helix: 0.82 (0.16), residues: 1171 sheet: -1.37 (0.27), residues: 354 loop : -2.24 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.031 0.002 TYR B 254 PHE 0.030 0.001 PHE A 137 TRP 0.028 0.002 TRP D 379 HIS 0.006 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00272 (28773) covalent geometry : angle 0.68547 (38954) SS BOND : bond 0.00371 ( 19) SS BOND : angle 1.81278 ( 38) hydrogen bonds : bond 0.03301 ( 810) hydrogen bonds : angle 4.74618 ( 2349) Misc. bond : bond 0.00791 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.022 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: A 154 MET cc_start: 0.9415 (mtm) cc_final: 0.8908 (mtp) REVERT: A 155 MET cc_start: 0.7883 (ttp) cc_final: 0.7404 (tmm) REVERT: A 347 MET cc_start: 0.9424 (ptt) cc_final: 0.9211 (ppp) REVERT: A 375 MET cc_start: 0.9081 (mmp) cc_final: 0.8795 (mpp) REVERT: A 415 MET cc_start: 0.8701 (tpt) cc_final: 0.8214 (mmm) REVERT: A 662 MET cc_start: 0.9643 (tmm) cc_final: 0.9346 (tmm) REVERT: A 834 MET cc_start: 0.9433 (tpt) cc_final: 0.9203 (tpp) REVERT: A 839 MET cc_start: 0.7478 (ptt) cc_final: 0.7228 (ptt) REVERT: B 142 MET cc_start: 0.6442 (mpp) cc_final: 0.6065 (mpp) REVERT: B 207 MET cc_start: 0.6943 (mmm) cc_final: 0.6694 (mmt) REVERT: B 386 MET cc_start: 0.4735 (mtp) cc_final: 0.4489 (mtp) REVERT: B 537 MET cc_start: 0.8963 (tmm) cc_final: 0.8618 (tmm) REVERT: B 561 MET cc_start: 0.9562 (mtm) cc_final: 0.9113 (mtm) REVERT: B 565 MET cc_start: 0.8828 (mmt) cc_final: 0.8508 (tpp) REVERT: B 566 LEU cc_start: 0.8995 (tt) cc_final: 0.8698 (mt) REVERT: B 654 MET cc_start: 0.9560 (tmm) cc_final: 0.9249 (tmm) REVERT: B 706 MET cc_start: 0.8925 (tmm) cc_final: 0.8585 (tmm) REVERT: B 809 MET cc_start: 0.9091 (pmm) cc_final: 0.7706 (tpt) REVERT: C 74 MET cc_start: 0.8359 (mtt) cc_final: 0.7767 (mmt) REVERT: C 154 MET cc_start: 0.9511 (mtm) cc_final: 0.9067 (mtp) REVERT: C 155 MET cc_start: 0.7109 (ttt) cc_final: 0.6502 (tmm) REVERT: C 375 MET cc_start: 0.8477 (mmp) cc_final: 0.7987 (mpp) REVERT: C 415 MET cc_start: 0.8957 (mmm) cc_final: 0.8739 (mmm) REVERT: C 436 MET cc_start: 0.8834 (mpp) cc_final: 0.8520 (mpp) REVERT: C 523 MET cc_start: 0.9045 (ttm) cc_final: 0.8772 (ttm) REVERT: C 723 MET cc_start: 0.9298 (tpt) cc_final: 0.8347 (tpt) REVERT: C 834 MET cc_start: 0.9462 (tpt) cc_final: 0.9180 (tpp) REVERT: D 54 HIS cc_start: 0.9271 (p-80) cc_final: 0.9016 (p-80) REVERT: D 132 MET cc_start: 0.7250 (tpp) cc_final: 0.7040 (tpp) REVERT: D 142 MET cc_start: 0.6100 (mpp) cc_final: 0.5569 (mpp) REVERT: D 207 MET cc_start: 0.6662 (mmm) cc_final: 0.6384 (mmt) REVERT: D 503 MET cc_start: 0.9487 (tpt) cc_final: 0.9160 (tpp) REVERT: D 537 MET cc_start: 0.8975 (tmm) cc_final: 0.8486 (tmm) REVERT: D 561 MET cc_start: 0.9337 (ptp) cc_final: 0.9068 (ptp) REVERT: D 565 MET cc_start: 0.8603 (mmt) cc_final: 0.8391 (tpp) REVERT: D 654 MET cc_start: 0.9496 (tmm) cc_final: 0.9217 (tmm) REVERT: D 706 MET cc_start: 0.8954 (tmm) cc_final: 0.8648 (tmm) REVERT: D 739 MET cc_start: 0.9597 (mmp) cc_final: 0.9392 (mmm) REVERT: D 809 MET cc_start: 0.9139 (pmm) cc_final: 0.7754 (tpt) REVERT: H 34 MET cc_start: 0.6259 (mmm) cc_final: 0.5631 (mmt) REVERT: H 83 MET cc_start: 0.5563 (mmp) cc_final: 0.4371 (mtm) REVERT: M 34 MET cc_start: 0.4561 (mmp) cc_final: 0.4027 (mtp) REVERT: M 83 MET cc_start: 0.3700 (mmp) cc_final: 0.2947 (mmp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1771 time to fit residues: 53.9472 Evaluate side-chains 164 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 59 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 216 optimal weight: 50.0000 chunk 223 optimal weight: 0.7980 chunk 247 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 104 optimal weight: 0.2980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN N 38 HIS N 49 HIS N 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.045719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.032450 restraints weight = 376199.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.032945 restraints weight = 235707.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.033302 restraints weight = 179326.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.033785 restraints weight = 149245.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.033930 restraints weight = 134681.472| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28793 Z= 0.160 Angle : 0.707 10.011 38992 Z= 0.367 Chirality : 0.045 0.248 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.465 55.670 3854 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.69 % Favored : 89.14 % Rotamer: Outliers : 0.03 % Allowed : 0.75 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 3.68 % Twisted General : 0.47 % 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: -1.51 (0.14), residues: 3528 helix: 0.89 (0.16), residues: 1173 sheet: -1.32 (0.25), residues: 385 loop : -2.24 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 98 TYR 0.020 0.002 TYR C 668 PHE 0.029 0.002 PHE A 137 TRP 0.032 0.002 TRP B 796 HIS 0.008 0.001 HIS N 49 Details of bonding type rmsd covalent geometry : bond 0.00346 (28773) covalent geometry : angle 0.70527 (38954) SS BOND : bond 0.00335 ( 19) SS BOND : angle 1.70513 ( 38) hydrogen bonds : bond 0.03392 ( 810) hydrogen bonds : angle 4.78176 ( 2349) Misc. bond : bond 0.00798 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.015 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: A 154 MET cc_start: 0.9445 (mtm) cc_final: 0.8951 (mtp) REVERT: A 155 MET cc_start: 0.7957 (ttp) cc_final: 0.7561 (tmm) REVERT: A 347 MET cc_start: 0.9438 (ptt) cc_final: 0.9230 (ppp) REVERT: A 375 MET cc_start: 0.9132 (mmp) cc_final: 0.8916 (mpp) REVERT: A 415 MET cc_start: 0.8856 (tpt) cc_final: 0.8372 (mmm) REVERT: A 523 MET cc_start: 0.9300 (ttm) cc_final: 0.9020 (ttm) REVERT: A 662 MET cc_start: 0.9663 (tmm) cc_final: 0.9379 (tmm) REVERT: A 834 MET cc_start: 0.9523 (tpt) cc_final: 0.9301 (tpp) REVERT: A 839 MET cc_start: 0.7494 (ptt) cc_final: 0.7262 (ptt) REVERT: B 142 MET cc_start: 0.6863 (mpp) cc_final: 0.6493 (mpp) REVERT: B 207 MET cc_start: 0.7053 (mmm) cc_final: 0.6797 (mmt) REVERT: B 307 MET cc_start: 0.8506 (ptt) cc_final: 0.8268 (ptt) REVERT: B 537 MET cc_start: 0.8856 (tmm) cc_final: 0.8562 (tmm) REVERT: B 561 MET cc_start: 0.9601 (mtm) cc_final: 0.9296 (mtp) REVERT: B 565 MET cc_start: 0.8849 (mmt) cc_final: 0.8535 (tpp) REVERT: B 566 LEU cc_start: 0.9007 (tt) cc_final: 0.8783 (mt) REVERT: B 654 MET cc_start: 0.9562 (tmm) cc_final: 0.9241 (tmm) REVERT: B 706 MET cc_start: 0.8988 (tmm) cc_final: 0.8625 (tmm) REVERT: B 809 MET cc_start: 0.9061 (pmm) cc_final: 0.7640 (tpt) REVERT: B 829 MET cc_start: 0.8635 (mtm) cc_final: 0.8259 (tmm) REVERT: C 74 MET cc_start: 0.8553 (mtt) cc_final: 0.8126 (mmm) REVERT: C 154 MET cc_start: 0.9530 (mtm) cc_final: 0.9078 (mtp) REVERT: C 155 MET cc_start: 0.7264 (ttt) cc_final: 0.6579 (tmm) REVERT: C 415 MET cc_start: 0.9049 (mmm) cc_final: 0.8527 (mmm) REVERT: C 436 MET cc_start: 0.8858 (mpp) cc_final: 0.8545 (mpp) REVERT: C 662 MET cc_start: 0.9693 (tmm) cc_final: 0.9491 (tmm) REVERT: C 834 MET cc_start: 0.9499 (tpt) cc_final: 0.9299 (tpp) REVERT: D 142 MET cc_start: 0.6313 (mpp) cc_final: 0.5757 (mpp) REVERT: D 207 MET cc_start: 0.6839 (mmm) cc_final: 0.6561 (mmt) REVERT: D 307 MET cc_start: 0.8256 (ptt) cc_final: 0.8015 (ptt) REVERT: D 503 MET cc_start: 0.9466 (tpt) cc_final: 0.9163 (tpp) REVERT: D 537 MET cc_start: 0.8972 (tmm) cc_final: 0.8646 (tmm) REVERT: D 565 MET cc_start: 0.8707 (mmt) cc_final: 0.8390 (tpp) REVERT: D 566 LEU cc_start: 0.9039 (tt) cc_final: 0.8797 (mt) REVERT: D 654 MET cc_start: 0.9540 (tmm) cc_final: 0.9237 (tmm) REVERT: D 706 MET cc_start: 0.8997 (tmm) cc_final: 0.8665 (tmm) REVERT: D 809 MET cc_start: 0.8985 (pmm) cc_final: 0.7862 (tpt) REVERT: H 34 MET cc_start: 0.6936 (mmm) cc_final: 0.5943 (mmt) REVERT: H 83 MET cc_start: 0.5748 (mmp) cc_final: 0.4690 (mtm) REVERT: M 83 MET cc_start: 0.3593 (mmp) cc_final: 0.2806 (mmp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1715 time to fit residues: 51.8534 Evaluate side-chains 161 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 201 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 349 optimal weight: 40.0000 chunk 336 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 221 optimal weight: 0.0470 chunk 274 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 overall best weight: 3.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.045806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033627 restraints weight = 372714.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.033575 restraints weight = 237465.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.034004 restraints weight = 172881.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.034403 restraints weight = 137275.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.034488 restraints weight = 124533.566| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28793 Z= 0.152 Angle : 0.706 10.867 38992 Z= 0.367 Chirality : 0.045 0.256 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.407 55.818 3854 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.80 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.44 % 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: -1.44 (0.14), residues: 3528 helix: 0.95 (0.16), residues: 1170 sheet: -1.29 (0.26), residues: 356 loop : -2.18 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 505 TYR 0.025 0.002 TYR L 95 PHE 0.027 0.002 PHE A 137 TRP 0.034 0.002 TRP D 796 HIS 0.008 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00330 (28773) covalent geometry : angle 0.70464 (38954) SS BOND : bond 0.00327 ( 19) SS BOND : angle 1.62732 ( 38) hydrogen bonds : bond 0.03387 ( 810) hydrogen bonds : angle 4.77025 ( 2349) Misc. bond : bond 0.00800 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.053 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: A 154 MET cc_start: 0.9448 (mtm) cc_final: 0.8928 (mtp) REVERT: A 155 MET cc_start: 0.8099 (ttp) cc_final: 0.7734 (tmm) REVERT: A 347 MET cc_start: 0.9430 (ptt) cc_final: 0.9225 (ppp) REVERT: A 375 MET cc_start: 0.9137 (mmp) cc_final: 0.8929 (mpp) REVERT: A 436 MET cc_start: 0.9100 (mpp) cc_final: 0.8881 (mpp) REVERT: A 523 MET cc_start: 0.9341 (ttm) cc_final: 0.9054 (ttm) REVERT: A 662 MET cc_start: 0.9637 (tmm) cc_final: 0.9353 (tmm) REVERT: A 834 MET cc_start: 0.9601 (tpt) cc_final: 0.9234 (tpp) REVERT: A 839 MET cc_start: 0.7435 (ptt) cc_final: 0.7213 (ptt) REVERT: B 142 MET cc_start: 0.6648 (mpp) cc_final: 0.6168 (mpp) REVERT: B 207 MET cc_start: 0.6674 (mmm) cc_final: 0.6390 (mmt) REVERT: B 537 MET cc_start: 0.8941 (tmm) cc_final: 0.8636 (tmm) REVERT: B 561 MET cc_start: 0.9532 (mtm) cc_final: 0.9216 (mtp) REVERT: B 654 MET cc_start: 0.9545 (tmm) cc_final: 0.9226 (tmm) REVERT: B 809 MET cc_start: 0.8870 (pmm) cc_final: 0.7604 (tpt) REVERT: B 829 MET cc_start: 0.8666 (mtm) cc_final: 0.8203 (tmm) REVERT: C 74 MET cc_start: 0.8549 (mtt) cc_final: 0.8117 (mmm) REVERT: C 154 MET cc_start: 0.9528 (mtm) cc_final: 0.9085 (mtp) REVERT: C 155 MET cc_start: 0.7323 (ttt) cc_final: 0.6621 (tmm) REVERT: C 375 MET cc_start: 0.8642 (mmp) cc_final: 0.8399 (mmm) REVERT: C 415 MET cc_start: 0.9074 (mmm) cc_final: 0.8529 (mmm) REVERT: C 436 MET cc_start: 0.8862 (mpp) cc_final: 0.8606 (mpp) REVERT: C 523 MET cc_start: 0.9217 (ttm) cc_final: 0.8795 (ttm) REVERT: C 662 MET cc_start: 0.9660 (tmm) cc_final: 0.9456 (tmm) REVERT: D 134 MET cc_start: 0.7066 (tpt) cc_final: 0.6854 (tpt) REVERT: D 142 MET cc_start: 0.6336 (mpp) cc_final: 0.5722 (mpp) REVERT: D 207 MET cc_start: 0.6783 (mmm) cc_final: 0.6506 (mmt) REVERT: D 307 MET cc_start: 0.8223 (ptt) cc_final: 0.7959 (ptt) REVERT: D 537 MET cc_start: 0.8936 (tmm) cc_final: 0.8577 (tmm) REVERT: D 565 MET cc_start: 0.8751 (mmt) cc_final: 0.8329 (tpt) REVERT: D 654 MET cc_start: 0.9509 (tmm) cc_final: 0.9210 (tmm) REVERT: D 706 MET cc_start: 0.9022 (tmm) cc_final: 0.8682 (tmm) REVERT: D 809 MET cc_start: 0.8990 (pmm) cc_final: 0.7834 (tpt) REVERT: H 34 MET cc_start: 0.6723 (mmm) cc_final: 0.5725 (mmt) REVERT: M 83 MET cc_start: 0.3690 (mmp) cc_final: 0.2890 (mmp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1724 time to fit residues: 53.2213 Evaluate side-chains 161 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 123 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 323 optimal weight: 0.3980 chunk 284 optimal weight: 0.0020 chunk 210 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 193 optimal weight: 0.5980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 HIS N 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.046992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.033678 restraints weight = 368390.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.034275 restraints weight = 229073.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.034774 restraints weight = 168923.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.035331 restraints weight = 138853.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.035404 restraints weight = 126198.601| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28793 Z= 0.116 Angle : 0.684 9.521 38992 Z= 0.353 Chirality : 0.045 0.264 4344 Planarity : 0.005 0.068 4947 Dihedral : 6.146 54.467 3854 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.69 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.47 % 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: -1.32 (0.15), residues: 3528 helix: 1.03 (0.16), residues: 1165 sheet: -1.30 (0.26), residues: 358 loop : -2.08 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.020 0.002 TYR C 668 PHE 0.024 0.001 PHE A 137 TRP 0.029 0.002 TRP D 796 HIS 0.007 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00252 (28773) covalent geometry : angle 0.68232 (38954) SS BOND : bond 0.00304 ( 19) SS BOND : angle 1.45669 ( 38) hydrogen bonds : bond 0.03229 ( 810) hydrogen bonds : angle 4.61830 ( 2349) Misc. bond : bond 0.00729 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6563.51 seconds wall clock time: 113 minutes 7.26 seconds (6787.26 seconds total)