Starting phenix.real_space_refine on Tue Jun 24 05:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7teb_25844/06_2025/7teb_25844.cif Found real_map, /net/cci-nas-00/data/ceres_data/7teb_25844/06_2025/7teb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7teb_25844/06_2025/7teb_25844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7teb_25844/06_2025/7teb_25844.map" model { file = "/net/cci-nas-00/data/ceres_data/7teb_25844/06_2025/7teb_25844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7teb_25844/06_2025/7teb_25844.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.054 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: 16.99, per 1000 atoms: 0.60 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: 7.12 Conformation dependent library (CDL) restraints added in 3.6 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: 3.34 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: 8.69 Time building geometry restraints manager: 8.38 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: 0.690 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: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 61.970 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.130 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.830 ------------------------------------------------------------------------------- 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 : 15.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.093 0.004 TRP C 402 HIS 0.024 0.003 HIS D 311 PHE 0.083 0.003 PHE D 176 TYR 0.059 0.003 TYR B 167 ARG 0.012 0.001 ARG D 375 Details of bonding type rmsd hydrogen bonds : bond 0.19828 ( 810) hydrogen bonds : angle 7.78748 ( 2349) SS BOND : bond 0.19707 ( 19) SS BOND : angle 14.18009 ( 38) covalent geometry : bond 0.00590 (28773) covalent geometry : angle 1.40959 (38954) 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 : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7480 (m) REVERT: A 463 THR cc_start: 0.5596 (OUTLIER) cc_final: 0.5371 (p) REVERT: A 586 LEU cc_start: 0.9139 (mp) cc_final: 0.8935 (tt) REVERT: A 598 LEU cc_start: 0.8636 (mt) cc_final: 0.8421 (mt) REVERT: A 723 MET cc_start: 0.6938 (tpt) cc_final: 0.6151 (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: 0.7151 (mpp) REVERT: B 54 HIS cc_start: 0.8165 (p-80) cc_final: 0.7687 (p-80) REVERT: B 207 MET cc_start: 0.6494 (mpp) cc_final: 0.5194 (mmm) REVERT: C 411 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5089 (mmt-90) REVERT: C 463 THR cc_start: 0.6370 (OUTLIER) cc_final: 0.5996 (p) REVERT: C 586 LEU cc_start: 0.9245 (mp) cc_final: 0.8919 (tt) REVERT: C 589 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8698 (pp) REVERT: C 723 MET cc_start: 0.6752 (tpt) cc_final: 0.6022 (tpt) REVERT: D 54 HIS cc_start: 0.8240 (p-80) cc_final: 0.7987 (p90) REVERT: D 207 MET cc_start: 0.6491 (mpp) cc_final: 0.4912 (mmm) REVERT: D 386 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.3730 (mmm) REVERT: D 829 MET cc_start: 0.8385 (tmm) cc_final: 0.8166 (tmm) REVERT: H 3 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8420 (mmmt) REVERT: H 34 MET cc_start: 0.5985 (mmm) cc_final: 0.5172 (mmm) REVERT: L 22 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.5052 (t) REVERT: L 28 ASP cc_start: 0.6889 (m-30) cc_final: 0.6181 (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: 0.7768 (tptt) REVERT: M 34 MET cc_start: 0.7112 (mmm) cc_final: 0.6750 (mmm) REVERT: M 80 TYR cc_start: 0.7544 (m-80) cc_final: 0.6904 (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: 0.6221 (t) REVERT: N 24 LYS cc_start: 0.9162 (mttt) cc_final: 0.8927 (mmmt) REVERT: N 50 TYR cc_start: 0.6699 (m-10) cc_final: 0.6315 (p90) REVERT: N 72 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8064 (m) outliers start: 119 outliers final: 23 residues processed: 362 average time/residue: 0.4842 time to fit residues: 277.6526 Evaluate side-chains 216 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 6.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 8.9990 chunk 268 optimal weight: 0.7980 chunk 148 optimal weight: 0.0000 chunk 91 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 107 optimal weight: 0.0270 chunk 168 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 321 optimal weight: 7.9990 overall best weight: 2.3646 ------------------------------------------------------------------------------- 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 ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS B 357 GLN B 495 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 67 HIS ** 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 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN L 38 HIS L 49 HIS L 55 GLN N 38 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.049238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.035814 restraints weight = 359356.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.036591 restraints weight = 219299.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.036990 restraints weight = 160269.220| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28793 Z= 0.168 Angle : 0.801 10.370 38992 Z= 0.427 Chirality : 0.048 0.292 4344 Planarity : 0.006 0.079 4947 Dihedral : 7.706 75.027 3854 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.58 % Favored : 89.85 % Rotamer: Outliers : 0.16 % Allowed : 6.07 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.12), residues: 3528 helix: -1.39 (0.13), residues: 1149 sheet: -1.55 (0.25), residues: 422 loop : -2.95 (0.12), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 151 HIS 0.013 0.001 HIS D 311 PHE 0.047 0.002 PHE A 42 TYR 0.023 0.002 TYR D 322 ARG 0.019 0.001 ARG M 98 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 810) hydrogen bonds : angle 5.60789 ( 2349) SS BOND : bond 0.00730 ( 19) SS BOND : angle 2.14933 ( 38) covalent geometry : bond 0.00357 (28773) covalent geometry : angle 0.79844 (38954) Misc. bond : bond 0.01028 ( 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 200 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 3.869 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: A 154 MET cc_start: 0.9267 (mtm) cc_final: 0.9027 (mtp) REVERT: A 375 MET cc_start: 0.8812 (mmp) cc_final: 0.8532 (mmm) REVERT: A 415 MET cc_start: 0.8473 (tpt) cc_final: 0.8257 (mmm) REVERT: A 523 MET cc_start: 0.9174 (ttm) cc_final: 0.8691 (ttm) REVERT: A 662 MET cc_start: 0.9607 (tmm) cc_final: 0.9352 (tmm) REVERT: B 54 HIS cc_start: 0.8602 (p-80) cc_final: 0.8385 (p-80) REVERT: B 73 MET cc_start: 0.8439 (tpp) cc_final: 0.8226 (tpp) REVERT: B 89 MET cc_start: 0.9562 (mmp) cc_final: 0.8778 (tpt) REVERT: B 201 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8900 (mm-30) REVERT: B 207 MET cc_start: 0.6831 (mpp) cc_final: 0.6341 (mmm) REVERT: B 386 MET cc_start: 0.4519 (mmp) cc_final: 0.4168 (mmm) REVERT: B 394 MET cc_start: 0.6554 (ptp) cc_final: 0.6256 (pmm) REVERT: B 537 MET cc_start: 0.8920 (tmm) cc_final: 0.8605 (tmm) REVERT: B 561 MET cc_start: 0.9485 (mtm) cc_final: 0.9043 (mtt) REVERT: B 654 MET cc_start: 0.9354 (tmm) cc_final: 0.9154 (tmm) REVERT: B 809 MET cc_start: 0.8228 (pmm) cc_final: 0.7796 (pmm) REVERT: C 154 MET cc_start: 0.9408 (mtm) cc_final: 0.9071 (mtp) REVERT: C 347 MET cc_start: 0.9448 (ptt) cc_final: 0.9132 (ppp) REVERT: C 375 MET cc_start: 0.8360 (mmp) cc_final: 0.8140 (mmm) REVERT: C 523 MET cc_start: 0.9214 (ttm) cc_final: 0.8730 (ttm) REVERT: C 839 MET cc_start: 0.8393 (ppp) cc_final: 0.8192 (ptt) REVERT: D 89 MET cc_start: 0.8948 (tpt) cc_final: 0.8314 (tpt) REVERT: D 207 MET cc_start: 0.7137 (mpp) cc_final: 0.6698 (mmm) REVERT: D 386 MET cc_start: 0.5296 (mmm) cc_final: 0.4841 (mmm) REVERT: D 394 MET cc_start: 0.6099 (ptp) cc_final: 0.5784 (pmm) REVERT: D 537 MET cc_start: 0.8789 (tmm) cc_final: 0.8464 (tmm) REVERT: D 818 MET cc_start: 0.9408 (tpt) cc_final: 0.9139 (mmm) REVERT: D 829 MET cc_start: 0.8960 (tmm) cc_final: 0.8715 (tmm) REVERT: H 34 MET cc_start: 0.6660 (mmm) cc_final: 0.5789 (mmm) REVERT: H 83 MET cc_start: 0.5786 (mmp) cc_final: 0.4686 (mtm) REVERT: M 34 MET cc_start: 0.5562 (mmm) cc_final: 0.5300 (mmm) REVERT: M 83 MET cc_start: 0.3734 (mmp) cc_final: 0.2924 (mmm) outliers start: 5 outliers final: 0 residues processed: 200 average time/residue: 0.5047 time to fit residues: 162.8672 Evaluate side-chains 163 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 281 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 244 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS B 145 GLN B 333 ASN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.047587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.035660 restraints weight = 365953.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.035552 restraints weight = 230038.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.035897 restraints weight = 162713.310| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28793 Z= 0.194 Angle : 0.762 9.910 38992 Z= 0.405 Chirality : 0.046 0.241 4344 Planarity : 0.005 0.076 4947 Dihedral : 7.249 71.211 3854 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.84 % Favored : 89.71 % Rotamer: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.13), residues: 3528 helix: -0.26 (0.15), residues: 1155 sheet: -1.40 (0.25), residues: 415 loop : -2.71 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 796 HIS 0.006 0.001 HIS A 392 PHE 0.027 0.002 PHE C 137 TYR 0.020 0.002 TYR B 167 ARG 0.008 0.001 ARG M 38 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 810) hydrogen bonds : angle 5.21847 ( 2349) SS BOND : bond 0.00754 ( 19) SS BOND : angle 2.14392 ( 38) covalent geometry : bond 0.00408 (28773) covalent geometry : angle 0.75980 (38954) Misc. bond : bond 0.00926 ( 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: 3 poor density : 189 time to evaluate : 3.111 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: A 154 MET cc_start: 0.9416 (mtm) cc_final: 0.9178 (mtp) REVERT: A 155 MET cc_start: 0.7044 (ttt) cc_final: 0.6480 (tmm) REVERT: A 375 MET cc_start: 0.8935 (mmp) cc_final: 0.8598 (mpp) REVERT: A 415 MET cc_start: 0.8723 (tpt) cc_final: 0.8434 (mmm) REVERT: A 662 MET cc_start: 0.9628 (tmm) cc_final: 0.9389 (tmm) REVERT: B 54 HIS cc_start: 0.9024 (p-80) cc_final: 0.8764 (p-80) REVERT: B 89 MET cc_start: 0.9584 (mmp) cc_final: 0.8856 (tpt) REVERT: B 132 MET cc_start: 0.6721 (mmt) cc_final: 0.6423 (tpp) REVERT: B 201 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8049 (pp20) REVERT: B 207 MET cc_start: 0.7315 (mpp) cc_final: 0.6698 (mmm) REVERT: B 386 MET cc_start: 0.4769 (mmp) cc_final: 0.4033 (mmm) REVERT: B 537 MET cc_start: 0.8933 (tmm) cc_final: 0.8549 (tmm) REVERT: B 561 MET cc_start: 0.9484 (mtm) cc_final: 0.8956 (ptp) REVERT: B 654 MET cc_start: 0.9438 (tmm) cc_final: 0.9064 (tmm) REVERT: B 809 MET cc_start: 0.8458 (pmm) cc_final: 0.8044 (pmm) REVERT: C 154 MET cc_start: 0.9513 (mtm) cc_final: 0.9139 (mtp) REVERT: C 155 MET cc_start: 0.6444 (ttt) cc_final: 0.6030 (tmm) REVERT: C 347 MET cc_start: 0.9433 (ptt) cc_final: 0.9231 (ppp) REVERT: C 375 MET cc_start: 0.8521 (mmp) cc_final: 0.8250 (mmm) REVERT: C 662 MET cc_start: 0.9642 (tmm) cc_final: 0.9364 (tmm) REVERT: C 839 MET cc_start: 0.8331 (ppp) cc_final: 0.8062 (ptt) REVERT: D 89 MET cc_start: 0.9078 (tpt) cc_final: 0.8528 (tpt) REVERT: D 207 MET cc_start: 0.7448 (mpp) cc_final: 0.6845 (mmm) REVERT: D 307 MET cc_start: 0.7857 (ptm) cc_final: 0.7569 (ptt) REVERT: D 386 MET cc_start: 0.5401 (mmm) cc_final: 0.5064 (mtp) REVERT: D 537 MET cc_start: 0.8821 (tmm) cc_final: 0.8419 (tmm) REVERT: D 654 MET cc_start: 0.9422 (tmm) cc_final: 0.9216 (tmm) REVERT: D 809 MET cc_start: 0.8536 (pmm) cc_final: 0.7391 (tpt) REVERT: D 818 MET cc_start: 0.9289 (tpt) cc_final: 0.8958 (mmm) REVERT: D 829 MET cc_start: 0.9097 (tmm) cc_final: 0.8764 (tmm) REVERT: M 83 MET cc_start: 0.4433 (mmp) cc_final: 0.3436 (mmm) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.4077 time to fit residues: 125.7140 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 : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 87 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 282 optimal weight: 0.2980 chunk 110 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 317 optimal weight: 0.0370 chunk 318 optimal weight: 8.9990 overall best weight: 2.6664 ------------------------------------------------------------------------------- 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 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS D 711 GLN N 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.047613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.037219 restraints weight = 368028.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.036872 restraints weight = 235016.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.037413 restraints weight = 159934.301| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28793 Z= 0.143 Angle : 0.700 11.784 38992 Z= 0.368 Chirality : 0.045 0.243 4344 Planarity : 0.005 0.070 4947 Dihedral : 6.837 61.252 3854 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.72 % Favored : 89.91 % Rotamer: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3528 helix: 0.28 (0.15), residues: 1145 sheet: -1.27 (0.27), residues: 363 loop : -2.48 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 796 HIS 0.006 0.001 HIS D 54 PHE 0.026 0.002 PHE M 29 TYR 0.022 0.002 TYR B 507 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 810) hydrogen bonds : angle 4.95919 ( 2349) SS BOND : bond 0.00319 ( 19) SS BOND : angle 1.56927 ( 38) covalent geometry : bond 0.00311 (28773) covalent geometry : angle 0.69859 (38954) Misc. bond : bond 0.00883 ( 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 188 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 3.149 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: A 154 MET cc_start: 0.9341 (mtm) cc_final: 0.9051 (mtp) REVERT: A 155 MET cc_start: 0.6903 (ttt) cc_final: 0.6429 (tmm) REVERT: A 375 MET cc_start: 0.8983 (mmp) cc_final: 0.8641 (mpp) REVERT: A 415 MET cc_start: 0.8718 (tpt) cc_final: 0.8442 (tpt) REVERT: A 523 MET cc_start: 0.8704 (ttm) cc_final: 0.8078 (ttm) REVERT: B 89 MET cc_start: 0.9572 (mmp) cc_final: 0.8897 (tpt) REVERT: B 207 MET cc_start: 0.7182 (mpp) cc_final: 0.6722 (mmm) REVERT: B 307 MET cc_start: 0.8389 (ptt) cc_final: 0.7919 (ptt) REVERT: B 386 MET cc_start: 0.4909 (mmp) cc_final: 0.3460 (tpp) REVERT: B 537 MET cc_start: 0.8992 (tmm) cc_final: 0.8711 (tmm) REVERT: B 561 MET cc_start: 0.9515 (mtm) cc_final: 0.9142 (mtp) REVERT: B 809 MET cc_start: 0.8518 (pmm) cc_final: 0.7313 (tpt) REVERT: C 74 MET cc_start: 0.8223 (mtt) cc_final: 0.7572 (mmm) REVERT: C 154 MET cc_start: 0.9530 (mtm) cc_final: 0.9114 (mtp) REVERT: C 155 MET cc_start: 0.6596 (ttt) cc_final: 0.6207 (tmm) REVERT: C 347 MET cc_start: 0.9420 (ptt) cc_final: 0.9176 (ppp) REVERT: C 375 MET cc_start: 0.8460 (mmp) cc_final: 0.8257 (mmm) REVERT: C 523 MET cc_start: 0.8743 (ttm) cc_final: 0.8112 (ttm) REVERT: C 662 MET cc_start: 0.9632 (tmm) cc_final: 0.9354 (tmm) REVERT: C 839 MET cc_start: 0.8181 (ppp) cc_final: 0.7873 (ptt) REVERT: D 54 HIS cc_start: 0.9073 (p-80) cc_final: 0.8787 (p-80) REVERT: D 89 MET cc_start: 0.9047 (tpt) cc_final: 0.8477 (tpt) REVERT: D 207 MET cc_start: 0.7230 (mpp) cc_final: 0.6842 (mmm) REVERT: D 307 MET cc_start: 0.7971 (ptm) cc_final: 0.7531 (ptt) REVERT: D 386 MET cc_start: 0.5601 (mmm) cc_final: 0.5223 (tpp) REVERT: D 537 MET cc_start: 0.8898 (tmm) cc_final: 0.8496 (tmm) REVERT: D 654 MET cc_start: 0.9452 (tmm) cc_final: 0.9218 (tmm) REVERT: D 706 MET cc_start: 0.8952 (tmm) cc_final: 0.8720 (tmm) REVERT: D 809 MET cc_start: 0.8963 (pmm) cc_final: 0.7439 (tpt) REVERT: D 829 MET cc_start: 0.9111 (tmm) cc_final: 0.8819 (tmm) REVERT: H 34 MET cc_start: 0.5149 (mmp) cc_final: 0.4602 (mmm) REVERT: M 83 MET cc_start: 0.3093 (mmp) cc_final: 0.2009 (mmm) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.4290 time to fit residues: 131.8816 Evaluate side-chains 156 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 332 optimal weight: 30.0000 chunk 243 optimal weight: 0.0670 chunk 111 optimal weight: 9.9990 chunk 333 optimal weight: 50.0000 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 349 optimal weight: 40.0000 chunk 132 optimal weight: 0.9990 chunk 156 optimal weight: 50.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- 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 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN B 218 ASN 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** N 38 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.046945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.033670 restraints weight = 368880.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.034303 restraints weight = 231331.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.035013 restraints weight = 169781.390| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28793 Z= 0.161 Angle : 0.711 9.078 38992 Z= 0.373 Chirality : 0.045 0.241 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.715 58.468 3854 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.12 % Favored : 89.60 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3528 helix: 0.52 (0.16), residues: 1165 sheet: -1.16 (0.28), residues: 336 loop : -2.39 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 796 HIS 0.025 0.001 HIS D 486 PHE 0.022 0.002 PHE C 137 TYR 0.020 0.002 TYR B 254 ARG 0.005 0.000 ARG N 61 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 810) hydrogen bonds : angle 4.91590 ( 2349) SS BOND : bond 0.00631 ( 19) SS BOND : angle 2.14726 ( 38) covalent geometry : bond 0.00348 (28773) covalent geometry : angle 0.70817 (38954) 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 184 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 3.107 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: A 154 MET cc_start: 0.9388 (mtm) cc_final: 0.9070 (mtp) REVERT: A 155 MET cc_start: 0.7266 (ttt) cc_final: 0.6721 (tmm) REVERT: A 375 MET cc_start: 0.9056 (mmp) cc_final: 0.8780 (mpp) REVERT: A 415 MET cc_start: 0.8779 (tpt) cc_final: 0.8487 (tpt) REVERT: A 523 MET cc_start: 0.8720 (ttm) cc_final: 0.8090 (ttm) REVERT: A 783 MET cc_start: 0.8077 (ttp) cc_final: 0.7782 (ttt) REVERT: B 132 MET cc_start: 0.6964 (tpp) cc_final: 0.6662 (tpp) REVERT: B 207 MET cc_start: 0.7177 (mpp) cc_final: 0.6481 (mmm) REVERT: B 307 MET cc_start: 0.8547 (ptt) cc_final: 0.8336 (ptm) REVERT: B 386 MET cc_start: 0.4900 (mmp) cc_final: 0.4469 (mmm) REVERT: B 503 MET cc_start: 0.9416 (tpt) cc_final: 0.9212 (tpp) REVERT: B 537 MET cc_start: 0.8974 (tmm) cc_final: 0.8693 (tmm) REVERT: B 561 MET cc_start: 0.9420 (mtm) cc_final: 0.9004 (mtp) REVERT: B 654 MET cc_start: 0.9429 (tmm) cc_final: 0.9066 (tmm) REVERT: B 809 MET cc_start: 0.8956 (pmm) cc_final: 0.7463 (tpt) REVERT: B 829 MET cc_start: 0.8769 (mtm) cc_final: 0.8535 (tmm) REVERT: C 74 MET cc_start: 0.8289 (mtt) cc_final: 0.7629 (mmm) REVERT: C 154 MET cc_start: 0.9569 (mtm) cc_final: 0.9146 (mtp) REVERT: C 155 MET cc_start: 0.6568 (ttt) cc_final: 0.6046 (tmm) REVERT: C 436 MET cc_start: 0.8798 (mpp) cc_final: 0.8537 (mpp) REVERT: C 523 MET cc_start: 0.8752 (ttm) cc_final: 0.8116 (ttm) REVERT: C 839 MET cc_start: 0.7875 (ppp) cc_final: 0.7586 (ptm) REVERT: D 89 MET cc_start: 0.9160 (tpt) cc_final: 0.8661 (tpt) REVERT: D 142 MET cc_start: 0.6894 (mpp) cc_final: 0.6169 (mpp) REVERT: D 207 MET cc_start: 0.7443 (mpp) cc_final: 0.7211 (mmm) REVERT: D 386 MET cc_start: 0.5860 (mmm) cc_final: 0.5442 (tpp) REVERT: D 537 MET cc_start: 0.8948 (tmm) cc_final: 0.8525 (tmm) REVERT: D 654 MET cc_start: 0.9458 (tmm) cc_final: 0.9164 (tmm) REVERT: D 706 MET cc_start: 0.9000 (tmm) cc_final: 0.8762 (tmm) REVERT: D 809 MET cc_start: 0.9013 (pmm) cc_final: 0.7467 (tpt) REVERT: D 818 MET cc_start: 0.9367 (tpt) cc_final: 0.9160 (mmm) REVERT: H 83 MET cc_start: 0.5607 (mmp) cc_final: 0.4277 (mtm) REVERT: M 34 MET cc_start: 0.6590 (mmt) cc_final: 0.6225 (mmm) REVERT: M 83 MET cc_start: 0.3456 (mmp) cc_final: 0.2655 (mmm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3791 time to fit residues: 113.6193 Evaluate side-chains 157 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 72 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 325 optimal weight: 6.9990 chunk 351 optimal weight: 30.0000 chunk 166 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 146 HIS A 217 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 495 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 D 159 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 HIS ** 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 = 0.3382 r_free = 0.3382 target = 0.046218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.035407 restraints weight = 375474.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.034989 restraints weight = 243564.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.035509 restraints weight = 169456.912| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28793 Z= 0.185 Angle : 0.723 9.256 38992 Z= 0.379 Chirality : 0.045 0.239 4344 Planarity : 0.005 0.070 4947 Dihedral : 6.673 57.148 3854 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.77 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3528 helix: 0.59 (0.16), residues: 1166 sheet: -1.39 (0.28), residues: 322 loop : -2.39 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 796 HIS 0.006 0.001 HIS D 486 PHE 0.020 0.002 PHE A 137 TYR 0.021 0.002 TYR B 507 ARG 0.013 0.001 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 810) hydrogen bonds : angle 4.87807 ( 2349) SS BOND : bond 0.00414 ( 19) SS BOND : angle 1.73629 ( 38) covalent geometry : bond 0.00394 (28773) covalent geometry : angle 0.72094 (38954) Misc. bond : bond 0.00816 ( 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 181 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 3.092 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: 0.9446 (mtm) cc_final: 0.9027 (mtp) REVERT: A 375 MET cc_start: 0.9102 (mmp) cc_final: 0.8861 (mpp) REVERT: A 415 MET cc_start: 0.8761 (tpt) cc_final: 0.8522 (mmm) REVERT: A 523 MET cc_start: 0.8756 (ttm) cc_final: 0.8106 (ttm) REVERT: A 662 MET cc_start: 0.9624 (tmm) cc_final: 0.9335 (tmm) REVERT: A 839 MET cc_start: 0.7477 (ptt) cc_final: 0.7197 (ptt) REVERT: B 132 MET cc_start: 0.6965 (tpp) cc_final: 0.6631 (tpp) REVERT: B 503 MET cc_start: 0.9442 (tpt) cc_final: 0.9219 (tpp) REVERT: B 537 MET cc_start: 0.8886 (tmm) cc_final: 0.8584 (tmm) REVERT: B 561 MET cc_start: 0.9409 (mtm) cc_final: 0.9014 (mtp) REVERT: B 654 MET cc_start: 0.9450 (tmm) cc_final: 0.9081 (tmm) REVERT: B 809 MET cc_start: 0.9068 (pmm) cc_final: 0.7509 (tpt) REVERT: B 829 MET cc_start: 0.8652 (mtm) cc_final: 0.8286 (tmm) REVERT: C 74 MET cc_start: 0.8259 (mtt) cc_final: 0.7622 (mmm) REVERT: C 154 MET cc_start: 0.9572 (mtm) cc_final: 0.9101 (mtp) REVERT: C 155 MET cc_start: 0.7338 (ttt) cc_final: 0.6583 (tmm) REVERT: C 375 MET cc_start: 0.8718 (mmp) cc_final: 0.8470 (mmm) REVERT: C 415 MET cc_start: 0.9008 (mmm) cc_final: 0.8636 (mmm) REVERT: C 436 MET cc_start: 0.8746 (mpp) cc_final: 0.8534 (mpp) REVERT: C 523 MET cc_start: 0.8782 (ttm) cc_final: 0.8139 (ttm) REVERT: C 662 MET cc_start: 0.9632 (tmm) cc_final: 0.9385 (tmm) REVERT: C 783 MET cc_start: 0.8346 (ttp) cc_final: 0.8109 (ttt) REVERT: D 89 MET cc_start: 0.9084 (tpt) cc_final: 0.8546 (tpt) REVERT: D 386 MET cc_start: 0.5565 (mmm) cc_final: 0.5317 (mtp) REVERT: D 537 MET cc_start: 0.8996 (tmm) cc_final: 0.8708 (tmm) REVERT: D 561 MET cc_start: 0.9354 (ptp) cc_final: 0.9151 (ptp) REVERT: D 654 MET cc_start: 0.9476 (tmm) cc_final: 0.9169 (tmm) REVERT: D 706 MET cc_start: 0.8977 (tmm) cc_final: 0.8692 (tmm) REVERT: D 809 MET cc_start: 0.9045 (pmm) cc_final: 0.7791 (tpt) REVERT: D 818 MET cc_start: 0.9339 (tpt) cc_final: 0.9036 (mmm) REVERT: H 83 MET cc_start: 0.5667 (mmp) cc_final: 0.4418 (mtm) REVERT: M 83 MET cc_start: 0.3217 (mmp) cc_final: 0.2610 (mmp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3746 time to fit residues: 111.3766 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 : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 214 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 263 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** A 146 HIS ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 D 357 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS 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 = 0.3346 r_free = 0.3346 target = 0.045183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.032366 restraints weight = 376883.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.032496 restraints weight = 247518.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.032906 restraints weight = 185702.298| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28793 Z= 0.222 Angle : 0.764 12.744 38992 Z= 0.399 Chirality : 0.046 0.235 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.780 57.316 3854 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.08 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3528 helix: 0.56 (0.15), residues: 1182 sheet: -1.38 (0.26), residues: 363 loop : -2.41 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP D 379 HIS 0.008 0.001 HIS A 392 PHE 0.026 0.002 PHE A 137 TYR 0.022 0.002 TYR B 507 ARG 0.005 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 810) hydrogen bonds : angle 4.99285 ( 2349) SS BOND : bond 0.00304 ( 19) SS BOND : angle 1.85358 ( 38) covalent geometry : bond 0.00463 (28773) covalent geometry : angle 0.76239 (38954) Misc. bond : bond 0.00840 ( 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 184 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 3.353 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: A 154 MET cc_start: 0.9346 (mtm) cc_final: 0.8910 (mtp) REVERT: A 523 MET cc_start: 0.8812 (ttm) cc_final: 0.8226 (ttm) REVERT: A 662 MET cc_start: 0.9589 (tmm) cc_final: 0.9281 (tmm) REVERT: B 142 MET cc_start: 0.7266 (pmm) cc_final: 0.7023 (pmm) REVERT: B 207 MET cc_start: 0.7080 (mmm) cc_final: 0.6843 (mmt) REVERT: B 561 MET cc_start: 0.9424 (mtm) cc_final: 0.9030 (mtp) REVERT: B 654 MET cc_start: 0.9435 (tmm) cc_final: 0.9079 (tmm) REVERT: B 809 MET cc_start: 0.9142 (pmm) cc_final: 0.7630 (tpt) REVERT: C 74 MET cc_start: 0.8326 (mtt) cc_final: 0.7725 (mmm) REVERT: C 154 MET cc_start: 0.9540 (mtm) cc_final: 0.9065 (mtp) REVERT: C 155 MET cc_start: 0.7104 (ttt) cc_final: 0.6429 (tmm) REVERT: C 375 MET cc_start: 0.8718 (mmp) cc_final: 0.8484 (mmm) REVERT: C 523 MET cc_start: 0.8863 (ttm) cc_final: 0.8297 (ttm) REVERT: C 662 MET cc_start: 0.9599 (tmm) cc_final: 0.9339 (tmm) REVERT: C 839 MET cc_start: 0.7490 (ptt) cc_final: 0.7044 (ptt) REVERT: D 73 MET cc_start: 0.7970 (tpp) cc_final: 0.7394 (tmm) REVERT: D 89 MET cc_start: 0.9154 (tpt) cc_final: 0.8674 (tpt) REVERT: D 142 MET cc_start: 0.6379 (mpp) cc_final: 0.5415 (mpp) REVERT: D 207 MET cc_start: 0.6754 (mmm) cc_final: 0.6465 (mmt) REVERT: D 307 MET cc_start: 0.8186 (ptt) cc_final: 0.7898 (ptt) REVERT: D 537 MET cc_start: 0.8803 (tmm) cc_final: 0.8587 (tmm) REVERT: D 654 MET cc_start: 0.9396 (tmm) cc_final: 0.9096 (tmm) REVERT: D 706 MET cc_start: 0.8870 (tmm) cc_final: 0.8502 (tmm) REVERT: D 809 MET cc_start: 0.9059 (pmm) cc_final: 0.7755 (tpt) REVERT: H 83 MET cc_start: 0.5557 (mmp) cc_final: 0.4357 (mtm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3874 time to fit residues: 117.4785 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 : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 182 optimal weight: 40.0000 chunk 167 optimal weight: 0.8980 chunk 264 optimal weight: 0.0980 chunk 331 optimal weight: 40.0000 chunk 315 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 N 49 HIS N 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.046060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.032861 restraints weight = 373453.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.033453 restraints weight = 232222.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.034067 restraints weight = 173272.434| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4999 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= 0.138 Angle : 0.706 9.024 38992 Z= 0.367 Chirality : 0.045 0.242 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.589 56.977 3854 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.08 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3528 helix: 0.77 (0.16), residues: 1165 sheet: -1.21 (0.28), residues: 325 loop : -2.34 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 379 HIS 0.007 0.001 HIS C 171 PHE 0.029 0.002 PHE A 137 TYR 0.026 0.002 TYR D 254 ARG 0.007 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 810) hydrogen bonds : angle 4.77038 ( 2349) SS BOND : bond 0.00325 ( 19) SS BOND : angle 1.77905 ( 38) covalent geometry : bond 0.00305 (28773) covalent geometry : angle 0.70375 (38954) Misc. bond : bond 0.00812 ( 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 182 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 3.133 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: 0.9460 (mtm) cc_final: 0.8985 (mtp) REVERT: A 347 MET cc_start: 0.9454 (ptt) cc_final: 0.9243 (ppp) REVERT: A 375 MET cc_start: 0.8815 (mpp) cc_final: 0.8481 (mpp) REVERT: A 415 MET cc_start: 0.8984 (tpt) cc_final: 0.8759 (tpt) REVERT: A 436 MET cc_start: 0.8895 (mpp) cc_final: 0.8693 (mpp) REVERT: A 523 MET cc_start: 0.9072 (ttm) cc_final: 0.8474 (ttm) REVERT: A 662 MET cc_start: 0.9640 (tmm) cc_final: 0.9339 (tmm) REVERT: A 834 MET cc_start: 0.9512 (tpt) cc_final: 0.9269 (tpp) REVERT: A 839 MET cc_start: 0.7458 (ptt) cc_final: 0.7200 (ptt) REVERT: B 142 MET cc_start: 0.7059 (pmm) cc_final: 0.6772 (pmm) REVERT: B 207 MET cc_start: 0.7012 (mmm) cc_final: 0.6772 (mmt) REVERT: B 386 MET cc_start: 0.5254 (mtp) cc_final: 0.4912 (ptm) REVERT: B 561 MET cc_start: 0.9459 (mtm) cc_final: 0.9087 (mtp) REVERT: B 654 MET cc_start: 0.9532 (tmm) cc_final: 0.9192 (tmm) REVERT: B 809 MET cc_start: 0.9115 (pmm) cc_final: 0.7624 (tpt) REVERT: B 829 MET cc_start: 0.8604 (mtm) cc_final: 0.8153 (tmm) REVERT: C 74 MET cc_start: 0.8302 (mtt) cc_final: 0.7723 (mmm) REVERT: C 154 MET cc_start: 0.9551 (mtm) cc_final: 0.9047 (mtp) REVERT: C 155 MET cc_start: 0.7132 (ttt) cc_final: 0.6574 (tmm) REVERT: C 375 MET cc_start: 0.8647 (mmp) cc_final: 0.8158 (mpp) REVERT: C 415 MET cc_start: 0.9156 (mmm) cc_final: 0.8710 (mmm) REVERT: C 436 MET cc_start: 0.8847 (mpp) cc_final: 0.8611 (mpp) REVERT: C 662 MET cc_start: 0.9645 (tmm) cc_final: 0.9390 (tmm) REVERT: C 834 MET cc_start: 0.9395 (tpt) cc_final: 0.9168 (tpp) REVERT: C 839 MET cc_start: 0.7455 (ptt) cc_final: 0.7005 (ptt) REVERT: D 89 MET cc_start: 0.9210 (tpt) cc_final: 0.8724 (tpt) REVERT: D 142 MET cc_start: 0.6562 (mpp) cc_final: 0.5991 (mpp) REVERT: D 207 MET cc_start: 0.6473 (mmm) cc_final: 0.6048 (mmt) REVERT: D 307 MET cc_start: 0.8258 (ptt) cc_final: 0.8011 (ptt) REVERT: D 537 MET cc_start: 0.8927 (tmm) cc_final: 0.8637 (tmm) REVERT: D 561 MET cc_start: 0.9363 (ptp) cc_final: 0.9157 (ptp) REVERT: D 565 MET cc_start: 0.8644 (mmt) cc_final: 0.8423 (tpp) REVERT: D 654 MET cc_start: 0.9516 (tmm) cc_final: 0.9220 (tmm) REVERT: D 706 MET cc_start: 0.9018 (tmm) cc_final: 0.8718 (tmm) REVERT: D 809 MET cc_start: 0.9046 (pmm) cc_final: 0.7855 (tpt) REVERT: H 83 MET cc_start: 0.5590 (mmp) cc_final: 0.4470 (mtm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3697 time to fit residues: 111.6561 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 : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 177 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 293 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** 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** ** L 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS N 49 HIS N 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.045953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034747 restraints weight = 372535.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.034403 restraints weight = 236498.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.034818 restraints weight = 166186.062| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5182 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= 0.146 Angle : 0.701 9.707 38992 Z= 0.364 Chirality : 0.045 0.239 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.486 55.663 3854 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.11 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 3.68 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3528 helix: 0.88 (0.16), residues: 1166 sheet: -1.41 (0.27), residues: 337 loop : -2.23 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 379 HIS 0.007 0.001 HIS C 171 PHE 0.028 0.002 PHE A 137 TYR 0.021 0.002 TYR C 668 ARG 0.004 0.000 ARG C 238 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 810) hydrogen bonds : angle 4.74636 ( 2349) SS BOND : bond 0.00284 ( 19) SS BOND : angle 1.73093 ( 38) covalent geometry : bond 0.00320 (28773) covalent geometry : angle 0.69889 (38954) Misc. bond : bond 0.00811 ( 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 179 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 3.407 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: A 74 MET cc_start: 0.8093 (mtt) cc_final: 0.7792 (mmm) REVERT: A 154 MET cc_start: 0.9440 (mtm) cc_final: 0.8992 (mtp) REVERT: A 347 MET cc_start: 0.9447 (ptt) cc_final: 0.9233 (ppp) REVERT: A 436 MET cc_start: 0.8939 (mpp) cc_final: 0.8723 (mpp) REVERT: A 662 MET cc_start: 0.9625 (tmm) cc_final: 0.9323 (tmm) REVERT: A 839 MET cc_start: 0.7449 (ptt) cc_final: 0.7218 (ptt) REVERT: B 142 MET cc_start: 0.7012 (pmm) cc_final: 0.6783 (pmm) REVERT: B 207 MET cc_start: 0.7017 (mmm) cc_final: 0.6780 (mmt) REVERT: B 537 MET cc_start: 0.8682 (tpt) cc_final: 0.8128 (tpt) REVERT: B 561 MET cc_start: 0.9465 (mtm) cc_final: 0.9088 (mtp) REVERT: B 654 MET cc_start: 0.9532 (tmm) cc_final: 0.9189 (tmm) REVERT: B 809 MET cc_start: 0.9096 (pmm) cc_final: 0.7639 (tpt) REVERT: B 829 MET cc_start: 0.8575 (mtm) cc_final: 0.8124 (tmm) REVERT: C 74 MET cc_start: 0.8367 (mtt) cc_final: 0.7834 (mmm) REVERT: C 154 MET cc_start: 0.9530 (mtm) cc_final: 0.9063 (mtp) REVERT: C 375 MET cc_start: 0.8516 (mmp) cc_final: 0.8289 (mmm) REVERT: C 415 MET cc_start: 0.9239 (mmm) cc_final: 0.8801 (mmm) REVERT: C 436 MET cc_start: 0.8861 (mpp) cc_final: 0.8615 (mpp) REVERT: C 523 MET cc_start: 0.9118 (ttm) cc_final: 0.8803 (ttm) REVERT: C 662 MET cc_start: 0.9633 (tmm) cc_final: 0.9431 (tmm) REVERT: C 834 MET cc_start: 0.9424 (tpt) cc_final: 0.9204 (tpp) REVERT: C 839 MET cc_start: 0.7372 (ptt) cc_final: 0.6983 (ptt) REVERT: D 54 HIS cc_start: 0.9278 (p-80) cc_final: 0.8942 (p-80) REVERT: D 73 MET cc_start: 0.7906 (tpt) cc_final: 0.7565 (tmm) REVERT: D 89 MET cc_start: 0.9104 (tpt) cc_final: 0.8568 (tpt) REVERT: D 132 MET cc_start: 0.7243 (tpt) cc_final: 0.6952 (tpp) REVERT: D 142 MET cc_start: 0.6278 (mpp) cc_final: 0.5861 (mpp) REVERT: D 207 MET cc_start: 0.6486 (mmm) cc_final: 0.6058 (mmt) REVERT: D 307 MET cc_start: 0.8231 (ptt) cc_final: 0.7973 (ptt) REVERT: D 561 MET cc_start: 0.9366 (ptp) cc_final: 0.9159 (ptp) REVERT: D 565 MET cc_start: 0.8667 (mmt) cc_final: 0.8259 (tpp) REVERT: D 566 LEU cc_start: 0.9135 (tt) cc_final: 0.8875 (mt) REVERT: D 654 MET cc_start: 0.9476 (tmm) cc_final: 0.9165 (tmm) REVERT: D 706 MET cc_start: 0.9023 (tmm) cc_final: 0.8702 (tmm) REVERT: D 809 MET cc_start: 0.9026 (pmm) cc_final: 0.7843 (tpt) REVERT: H 34 MET cc_start: 0.5953 (mmm) cc_final: 0.5531 (mmm) REVERT: H 83 MET cc_start: 0.5545 (mmp) cc_final: 0.4387 (mtm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3791 time to fit residues: 113.2700 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 : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 86 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 97 optimal weight: 20.0000 chunk 309 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** 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** ** L 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3373 r_free = 0.3373 target = 0.045904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.032783 restraints weight = 373753.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.033305 restraints weight = 235525.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.033636 restraints weight = 175546.913| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5351 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= 0.146 Angle : 0.700 10.757 38992 Z= 0.364 Chirality : 0.045 0.256 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.404 55.554 3854 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.88 % Favored : 88.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3528 helix: 0.95 (0.16), residues: 1166 sheet: -1.34 (0.27), residues: 341 loop : -2.22 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 379 HIS 0.011 0.001 HIS N 49 PHE 0.024 0.002 PHE A 137 TYR 0.020 0.002 TYR C 668 ARG 0.006 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 810) hydrogen bonds : angle 4.72223 ( 2349) SS BOND : bond 0.00304 ( 19) SS BOND : angle 1.59996 ( 38) covalent geometry : bond 0.00320 (28773) covalent geometry : angle 0.69863 (38954) Misc. bond : bond 0.00793 ( 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 179 residues out of total 3092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 3.076 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: A 154 MET cc_start: 0.9432 (mtm) cc_final: 0.9009 (mtp) REVERT: A 347 MET cc_start: 0.9446 (ptt) cc_final: 0.9243 (ppp) REVERT: A 415 MET cc_start: 0.8786 (tpt) cc_final: 0.8542 (tpt) REVERT: A 436 MET cc_start: 0.8973 (mpp) cc_final: 0.8725 (mpp) REVERT: A 523 MET cc_start: 0.9169 (ttm) cc_final: 0.8789 (ttm) REVERT: A 662 MET cc_start: 0.9624 (tmm) cc_final: 0.9323 (tmm) REVERT: A 839 MET cc_start: 0.7506 (ptt) cc_final: 0.7301 (ptt) REVERT: B 142 MET cc_start: 0.7164 (pmm) cc_final: 0.6778 (pmm) REVERT: B 207 MET cc_start: 0.6820 (mmm) cc_final: 0.6534 (mmt) REVERT: B 537 MET cc_start: 0.8675 (tpt) cc_final: 0.8136 (tpt) REVERT: B 561 MET cc_start: 0.9455 (mtm) cc_final: 0.9086 (mtp) REVERT: B 654 MET cc_start: 0.9524 (tmm) cc_final: 0.9160 (tmm) REVERT: B 809 MET cc_start: 0.9082 (pmm) cc_final: 0.7637 (tpt) REVERT: B 829 MET cc_start: 0.8694 (mtm) cc_final: 0.8193 (tmm) REVERT: C 74 MET cc_start: 0.8392 (mtt) cc_final: 0.7843 (mmm) REVERT: C 154 MET cc_start: 0.9551 (mtm) cc_final: 0.9084 (mtp) REVERT: C 375 MET cc_start: 0.8516 (mmp) cc_final: 0.8294 (mmm) REVERT: C 415 MET cc_start: 0.9252 (mmm) cc_final: 0.8789 (mmm) REVERT: C 436 MET cc_start: 0.8900 (mpp) cc_final: 0.8661 (mpp) REVERT: C 523 MET cc_start: 0.9248 (ttm) cc_final: 0.8808 (ttm) REVERT: C 662 MET cc_start: 0.9627 (tmm) cc_final: 0.9426 (tmm) REVERT: C 834 MET cc_start: 0.9502 (tpt) cc_final: 0.9245 (tpp) REVERT: C 839 MET cc_start: 0.7338 (ptt) cc_final: 0.6943 (ptt) REVERT: D 89 MET cc_start: 0.9154 (tpt) cc_final: 0.8621 (tpt) REVERT: D 134 MET cc_start: 0.6578 (tpt) cc_final: 0.6115 (tpt) REVERT: D 142 MET cc_start: 0.5667 (mpp) cc_final: 0.5044 (mpp) REVERT: D 207 MET cc_start: 0.6555 (mmm) cc_final: 0.6121 (mmt) REVERT: D 307 MET cc_start: 0.8273 (ptt) cc_final: 0.8024 (ptt) REVERT: D 386 MET cc_start: 0.5837 (ttp) cc_final: 0.4986 (ptm) REVERT: D 565 MET cc_start: 0.8663 (mmt) cc_final: 0.8349 (tpp) REVERT: D 654 MET cc_start: 0.9481 (tmm) cc_final: 0.9149 (tmm) REVERT: D 706 MET cc_start: 0.9026 (tmm) cc_final: 0.8700 (tmm) REVERT: D 809 MET cc_start: 0.9045 (pmm) cc_final: 0.7862 (tpt) REVERT: H 34 MET cc_start: 0.6198 (mmm) cc_final: 0.5871 (mmm) REVERT: H 83 MET cc_start: 0.5565 (mmp) cc_final: 0.4406 (mtm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3858 time to fit residues: 115.4676 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 : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 141 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 340 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS C 28 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN N 38 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.045649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.034411 restraints weight = 376419.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.033755 restraints weight = 245366.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.034152 restraints weight = 172960.292| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5601 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= 0.154 Angle : 0.704 10.593 38992 Z= 0.366 Chirality : 0.045 0.261 4344 Planarity : 0.005 0.071 4947 Dihedral : 6.360 55.191 3854 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.83 % Favored : 89.00 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3528 helix: 0.95 (0.16), residues: 1177 sheet: -1.38 (0.27), residues: 347 loop : -2.18 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 796 HIS 0.007 0.001 HIS C 171 PHE 0.024 0.002 PHE A 137 TYR 0.022 0.002 TYR B 507 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 810) hydrogen bonds : angle 4.73099 ( 2349) SS BOND : bond 0.00289 ( 19) SS BOND : angle 1.58990 ( 38) covalent geometry : bond 0.00332 (28773) covalent geometry : angle 0.70293 (38954) Misc. bond : bond 0.00762 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11202.45 seconds wall clock time: 197 minutes 29.22 seconds (11849.22 seconds total)