Starting phenix.real_space_refine on Tue May 5 00:58:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrf_61753/05_2026/9jrf_61753.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrf_61753/05_2026/9jrf_61753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jrf_61753/05_2026/9jrf_61753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrf_61753/05_2026/9jrf_61753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jrf_61753/05_2026/9jrf_61753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrf_61753/05_2026/9jrf_61753.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 131 5.16 5 C 15665 2.51 5 N 4225 2.21 5 O 4615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24636 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 6259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6259 Classifications: {'peptide': 795} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 767} Chain breaks: 2 Chain: "C" Number of atoms: 6267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6267 Classifications: {'peptide': 796} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 768} Chain breaks: 2 Chain: "D" Number of atoms: 6010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 765, 5999 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 737} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 765, 5999 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 737} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 6106 Chain: "A" Number of atoms: 6072 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 772, 6061 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 744} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 772, 6061 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 744} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 6172 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG D 226 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG D 226 " occ=0.48 residue: pdb=" N AARG A 226 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG A 226 " occ=0.48 Time building chain proxies: 8.01, per 1000 atoms: 0.33 Number of scatterers: 24636 At special positions: 0 Unit cell: (136.74, 122.12, 195.22, 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 131 16.00 O 4615 8.00 N 4225 7.00 C 15665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 128 " distance=2.04 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 306 " distance=2.04 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 128 " distance=2.04 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 306 " distance=2.04 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 351 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 128 " distance=2.05 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 811 " 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=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN B 901 " pdb=" CB DSN C 901 " pdb=" CB DSN D 901 " pdb=" CB DSN A 901 " Number of C-beta restraints generated: 5886 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 25 sheets defined 47.3% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 34 through 52 Processing helix chain 'B' and resid 71 through 85 removed outlier: 3.504A pdb=" N THR B 84 " --> pdb=" O CYS B 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.519A pdb=" N ALA B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.549A pdb=" N VAL B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.551A pdb=" N ASP B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 317 through 340 Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 502 through 509 removed outlier: 4.249A pdb=" N GLU B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 removed outlier: 3.790A pdb=" N VAL B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 530 " --> pdb=" O ARG B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 588 Proline residue: B 574 - end of helix removed outlier: 4.315A pdb=" N PHE B 581 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 661 removed outlier: 3.600A pdb=" N ARG B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 661 " --> pdb=" O THR B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 694 Processing helix chain 'B' and resid 703 through 713 removed outlier: 3.927A pdb=" N GLU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 717 Processing helix chain 'B' and resid 727 through 732 removed outlier: 4.071A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 753 removed outlier: 3.754A pdb=" N ASP B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 795 Processing helix chain 'B' and resid 796 through 805 removed outlier: 4.313A pdb=" N LEU B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 818 Processing helix chain 'B' and resid 831 through 857 Processing helix chain 'C' and resid 34 through 52 Processing helix chain 'C' and resid 71 through 85 removed outlier: 3.503A pdb=" N THR C 84 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 removed outlier: 3.519A pdb=" N ALA C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.548A pdb=" N VAL C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.550A pdb=" N ASP C 222 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 317 through 340 Processing helix chain 'C' and resid 361 through 371 Processing helix chain 'C' and resid 466 through 479 removed outlier: 3.704A pdb=" N ALA C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 523 through 530 Processing helix chain 'C' and resid 562 through 589 Proline residue: C 574 - end of helix Processing helix chain 'C' and resid 627 through 659 removed outlier: 3.757A pdb=" N ASN C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 652 " --> pdb=" O TYR C 648 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 662 No H-bonds generated for 'chain 'C' and resid 660 through 662' Processing helix chain 'C' and resid 667 through 673 removed outlier: 3.650A pdb=" N SER C 672 " --> pdb=" O PHE C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 703 through 713 Processing helix chain 'C' and resid 724 through 732 Processing helix chain 'C' and resid 743 through 753 removed outlier: 3.563A pdb=" N ASP C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 795 removed outlier: 4.504A pdb=" N ARG C 787 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 805 removed outlier: 3.670A pdb=" N TRP C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 856 removed outlier: 3.775A pdb=" N PHE C 831 " --> pdb=" O LYS C 827 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C 833 " --> pdb=" O HIS C 829 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 853 " --> pdb=" O ALA C 849 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 856 " --> pdb=" O GLU C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 50 removed outlier: 3.675A pdb=" N LEU D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 148 through 160 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 200 through 212 removed outlier: 3.996A pdb=" N PHE D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 208 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 317 through 340 Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 466 through 469 Processing helix chain 'D' and resid 470 through 479 Processing helix chain 'D' and resid 502 through 510 removed outlier: 3.953A pdb=" N GLU D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 508 " --> pdb=" O MET D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 554 through 558 Processing helix chain 'D' and resid 562 through 587 removed outlier: 4.334A pdb=" N ILE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Proline residue: D 574 - end of helix Processing helix chain 'D' and resid 627 through 660 removed outlier: 3.827A pdb=" N ARG D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 672 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.814A pdb=" N LYS D 694 " --> pdb=" O TYR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 708 removed outlier: 3.745A pdb=" N ALA D 706 " --> pdb=" O ASP D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing helix chain 'D' and resid 724 through 734 removed outlier: 4.833A pdb=" N ARG D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 753 Processing helix chain 'D' and resid 779 through 795 removed outlier: 4.373A pdb=" N LEU D 783 " --> pdb=" O PRO D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 805 removed outlier: 4.225A pdb=" N VAL D 799 " --> pdb=" O GLY D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 830 No H-bonds generated for 'chain 'D' and resid 828 through 830' Processing helix chain 'D' and resid 831 through 852 removed outlier: 3.851A pdb=" N LEU D 842 " --> pdb=" O LEU D 838 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.675A pdb=" N LEU A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.995A pdb=" N PHE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 317 through 340 Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.554A pdb=" N ALA A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.754A pdb=" N LEU A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 562 through 587 Proline residue: A 574 - end of helix Processing helix chain 'A' and resid 627 through 659 removed outlier: 3.724A pdb=" N SER A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 714 through 718 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.665A pdb=" N GLY A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 753 removed outlier: 3.623A pdb=" N ASP A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 795 removed outlier: 3.640A pdb=" N GLN A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 812 through 817 Processing helix chain 'A' and resid 827 through 856 removed outlier: 4.542A pdb=" N PHE A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 67 removed outlier: 6.121A pdb=" N ILE B 24 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER B 63 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 26 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS B 65 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA B 28 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE B 67 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 30 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N VAL B 91 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 27 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N SER B 93 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 29 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS B 113 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 191 through 196 removed outlier: 7.517A pdb=" N LYS B 164 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE B 228 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 166 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU B 230 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE B 168 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET B 278 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY B 398 " --> pdb=" O LYS B 411 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS B 411 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR B 400 " --> pdb=" O MET B 409 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N MET B 409 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER B 402 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS B 407 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 376 Processing sheet with id=AA5, first strand: chain 'B' and resid 483 through 486 removed outlier: 3.833A pdb=" N LEU B 515 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 741 through 742 removed outlier: 3.929A pdb=" N VAL B 541 " --> pdb=" O ASN B 763 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 763 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 67 removed outlier: 6.120A pdb=" N ILE C 24 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER C 63 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 26 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS C 65 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 28 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE C 67 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE C 30 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL C 91 " --> pdb=" O HIS C 25 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY C 27 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER C 93 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 29 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS C 113 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 191 through 196 removed outlier: 7.516A pdb=" N LYS C 164 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE C 228 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 166 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU C 230 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 168 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET C 278 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY C 398 " --> pdb=" O LYS C 411 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS C 411 " --> pdb=" O GLY C 398 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR C 400 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N MET C 409 " --> pdb=" O THR C 400 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N SER C 402 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 407 " --> pdb=" O SER C 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AB1, first strand: chain 'C' and resid 373 through 376 Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 443 removed outlier: 5.457A pdb=" N VAL C 441 " --> pdb=" O TYR C 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AB4, first strand: chain 'C' and resid 739 through 742 removed outlier: 3.618A pdb=" N ILE C 543 " --> pdb=" O ILE C 761 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.444A pdb=" N THR C 681 " --> pdb=" O VAL C 722 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 60 through 67 removed outlier: 6.362A pdb=" N ILE D 24 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER D 63 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 26 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LYS D 65 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA D 28 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE D 67 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE D 30 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N VAL D 91 " --> pdb=" O HIS D 25 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY D 27 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER D 93 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 29 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU D 90 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL D 116 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS D 113 " --> pdb=" O LEU D 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 191 through 197 removed outlier: 7.339A pdb=" N LYS D 164 " --> pdb=" O AARG D 226 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE D 228 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 166 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU D 230 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE D 168 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY D 398 " --> pdb=" O LYS D 411 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS D 411 " --> pdb=" O GLY D 398 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 373 through 376 Processing sheet with id=AB9, first strand: chain 'D' and resid 537 through 538 removed outlier: 4.821A pdb=" N MET D 537 " --> pdb=" O TYR D 770 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR D 770 " --> pdb=" O MET D 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 678 through 680 removed outlier: 6.936A pdb=" N SER D 678 " --> pdb=" O ALA D 738 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N LEU D 740 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY D 680 " --> pdb=" O LEU D 740 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N ASP D 742 " --> pdb=" O GLY D 680 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N TYR D 737 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS D 546 " --> pdb=" O TYR D 737 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 739 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 60 through 67 removed outlier: 6.362A pdb=" N ILE A 24 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER A 63 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 26 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LYS A 65 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA A 28 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE A 67 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE A 30 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N VAL A 91 " --> pdb=" O HIS A 25 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY A 27 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER A 93 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 29 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 90 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 116 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR A 92 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS A 113 " --> pdb=" O LEU A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 191 through 197 removed outlier: 7.337A pdb=" N LYS A 164 " --> pdb=" O AARG A 226 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE A 228 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 166 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A 230 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 168 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A 398 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS A 411 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 373 through 376 Processing sheet with id=AC5, first strand: chain 'A' and resid 442 through 443 Processing sheet with id=AC6, first strand: chain 'A' and resid 450 through 451 removed outlier: 4.174A pdb=" N LYS A 464 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 544 through 546 1121 hydrogen bonds defined for protein. 3257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8025 1.34 - 1.46: 5743 1.46 - 1.58: 11154 1.58 - 1.71: 0 1.71 - 1.83: 212 Bond restraints: 25134 Sorted by residual: bond pdb=" CA THR A 140 " pdb=" CB THR A 140 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.35e-02 5.49e+03 3.45e+00 bond pdb=" CA THR D 140 " pdb=" CB THR D 140 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.35e-02 5.49e+03 3.13e+00 bond pdb=" CA ILE C 175 " pdb=" CB ILE C 175 " ideal model delta sigma weight residual 1.542 1.564 -0.022 1.28e-02 6.10e+03 2.88e+00 bond pdb=" CA ALA D 75 " pdb=" CB ALA D 75 " ideal model delta sigma weight residual 1.528 1.503 0.025 1.56e-02 4.11e+03 2.60e+00 bond pdb=" CA ILE B 175 " pdb=" CB ILE B 175 " ideal model delta sigma weight residual 1.542 1.563 -0.020 1.28e-02 6.10e+03 2.55e+00 ... (remaining 25129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 33332 2.36 - 4.72: 646 4.72 - 7.08: 58 7.08 - 9.44: 4 9.44 - 11.80: 3 Bond angle restraints: 34043 Sorted by residual: angle pdb=" N ARG A 353 " pdb=" CA ARG A 353 " pdb=" C ARG A 353 " ideal model delta sigma weight residual 111.82 121.56 -9.74 1.16e+00 7.43e-01 7.04e+01 angle pdb=" N ARG D 353 " pdb=" CA ARG D 353 " pdb=" C ARG D 353 " ideal model delta sigma weight residual 111.82 121.47 -9.65 1.16e+00 7.43e-01 6.92e+01 angle pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" C ILE A 352 " ideal model delta sigma weight residual 110.72 116.14 -5.42 1.01e+00 9.80e-01 2.88e+01 angle pdb=" N ILE D 352 " pdb=" CA ILE D 352 " pdb=" C ILE D 352 " ideal model delta sigma weight residual 110.72 116.08 -5.36 1.01e+00 9.80e-01 2.82e+01 angle pdb=" N VAL A 204 " pdb=" CA VAL A 204 " pdb=" C VAL A 204 " ideal model delta sigma weight residual 110.30 115.05 -4.75 9.70e-01 1.06e+00 2.40e+01 ... (remaining 34038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14029 17.95 - 35.90: 872 35.90 - 53.85: 157 53.85 - 71.81: 27 71.81 - 89.76: 10 Dihedral angle restraints: 15095 sinusoidal: 6001 harmonic: 9094 Sorted by residual: dihedral pdb=" CB CYS A 756 " pdb=" SG CYS A 756 " pdb=" SG CYS A 811 " pdb=" CB CYS A 811 " ideal model delta sinusoidal sigma weight residual 93.00 -178.09 -88.91 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS D 756 " pdb=" SG CYS D 756 " pdb=" SG CYS D 811 " pdb=" CB CYS D 811 " ideal model delta sinusoidal sigma weight residual 93.00 154.15 -61.15 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS B 756 " pdb=" SG CYS B 756 " pdb=" SG CYS B 811 " pdb=" CB CYS B 811 " ideal model delta sinusoidal sigma weight residual -86.00 -143.96 57.96 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 15092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3127 0.050 - 0.099: 562 0.099 - 0.149: 166 0.149 - 0.198: 7 0.198 - 0.248: 6 Chirality restraints: 3868 Sorted by residual: chirality pdb=" CA ILE C 24 " pdb=" N ILE C 24 " pdb=" C ILE C 24 " pdb=" CB ILE C 24 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE B 24 " pdb=" N ILE B 24 " pdb=" C ILE B 24 " pdb=" CB ILE B 24 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG A 353 " pdb=" N ARG A 353 " pdb=" C ARG A 353 " pdb=" CB ARG A 353 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3865 not shown) Planarity restraints: 4333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 459 " -0.071 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO A 460 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 447 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO D 448 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 448 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 448 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 190 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C LEU D 190 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU D 190 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP D 191 " 0.013 2.00e-02 2.50e+03 ... (remaining 4330 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 310 2.66 - 3.22: 23717 3.22 - 3.78: 37200 3.78 - 4.34: 50832 4.34 - 4.90: 80872 Nonbonded interactions: 192931 Sorted by model distance: nonbonded pdb=" NH2 ARG A 787 " pdb=" OE1 GLU A 790 " model vdw 2.096 3.120 nonbonded pdb=" OH TYR D 539 " pdb=" OD1 ASP D 742 " model vdw 2.209 3.040 nonbonded pdb=" O GLY A 465 " pdb=" N ASP A 469 " model vdw 2.217 3.120 nonbonded pdb=" O ASN C 350 " pdb=" OG1 THR C 356 " model vdw 2.250 3.040 nonbonded pdb=" O ASN B 350 " pdb=" OG1 THR B 356 " model vdw 2.251 3.040 ... (remaining 192926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 225 or resid 227 through 424 or resid 433 throu \ gh 587 or resid 626 through 852 or resid 901)) selection = (chain 'B' and (resid 22 through 51 or resid 57 through 225 or resid 227 through \ 288 or (resid 299 and (name N or name CA or name C or name O or name CB )) or r \ esid 300 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 399 or resid 406 through 424 or resid 433 throu \ gh 587 or resid 626 through 852 or resid 901)) selection = (chain 'C' and (resid 22 through 51 or resid 57 through 225 or resid 227 through \ 288 or (resid 299 and (name N or name CA or name C or name O or name CB )) or r \ esid 300 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 399 or resid 406 through 424 or resid 433 throu \ gh 587 or resid 626 through 852 or resid 901)) selection = (chain 'D' and (resid 22 through 225 or resid 227 through 587 or resid 626 throu \ gh 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 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: 6.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.320 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3809 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25148 Z= 0.257 Angle : 0.844 26.599 34071 Z= 0.527 Chirality : 0.043 0.248 3868 Planarity : 0.004 0.109 4333 Dihedral : 12.255 89.757 9167 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 1.00 % Allowed : 1.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3098 helix: 0.61 (0.13), residues: 1387 sheet: -0.72 (0.24), residues: 367 loop : -1.00 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 787 TYR 0.017 0.002 TYR A 173 PHE 0.024 0.001 PHE C 655 TRP 0.022 0.001 TRP A 709 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00407 (25134) covalent geometry : angle 0.81156 (34043) SS BOND : bond 0.00840 ( 14) SS BOND : angle 8.16271 ( 28) hydrogen bonds : bond 0.18572 ( 1121) hydrogen bonds : angle 5.69348 ( 3257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 482 time to evaluate : 0.924 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: B 517 ILE cc_start: 0.8624 (pt) cc_final: 0.8371 (mm) REVERT: B 634 MET cc_start: 0.6499 (mmp) cc_final: 0.5666 (tpt) REVERT: B 661 MET cc_start: 0.8002 (tmm) cc_final: 0.7631 (tmm) REVERT: C 258 VAL cc_start: 0.5099 (t) cc_final: 0.4806 (t) REVERT: C 365 MET cc_start: -0.1292 (tpp) cc_final: -0.1704 (tpt) REVERT: C 430 MET cc_start: -0.0367 (ptp) cc_final: -0.1226 (mmm) REVERT: C 463 TYR cc_start: 0.4681 (p90) cc_final: 0.4305 (p90) REVERT: C 504 MET cc_start: 0.4382 (ttt) cc_final: 0.3946 (tpp) REVERT: D 373 HIS cc_start: 0.4980 (OUTLIER) cc_final: 0.4338 (p-80) REVERT: D 482 TYR cc_start: 0.1574 (p90) cc_final: 0.1089 (p90) REVERT: D 634 MET cc_start: 0.6782 (mpp) cc_final: 0.6262 (tmm) REVERT: D 671 LEU cc_start: 0.8985 (tp) cc_final: 0.8702 (tt) REVERT: A 677 MET cc_start: 0.4275 (tpt) cc_final: 0.3993 (tpt) outliers start: 27 outliers final: 0 residues processed: 507 average time/residue: 0.1906 time to fit residues: 144.5580 Evaluate side-chains 247 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.0070 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.0970 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 241 ASN B 272 HIS B 455 ASN C 179 GLN C 200 ASN C 272 HIS C 283 GLN C 775 GLN D 332 ASN D 497 HIS D 502 ASN D 786 GLN A 195 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.151344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.134173 restraints weight = 232295.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.136465 restraints weight = 295518.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.137657 restraints weight = 132372.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.137912 restraints weight = 94134.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.138188 restraints weight = 84711.534| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4497 r_free = 0.4497 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4497 r_free = 0.4497 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5089 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25148 Z= 0.169 Angle : 0.646 14.013 34071 Z= 0.339 Chirality : 0.043 0.299 3868 Planarity : 0.005 0.092 4333 Dihedral : 4.792 44.193 3376 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3098 helix: 1.14 (0.14), residues: 1394 sheet: -0.70 (0.23), residues: 407 loop : -0.86 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 353 TYR 0.021 0.002 TYR A 173 PHE 0.032 0.002 PHE B 181 TRP 0.054 0.002 TRP A 709 HIS 0.008 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00367 (25134) covalent geometry : angle 0.64534 (34043) SS BOND : bond 0.00179 ( 14) SS BOND : angle 1.16724 ( 28) hydrogen bonds : bond 0.05463 ( 1121) hydrogen bonds : angle 4.58990 ( 3257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 MET cc_start: 0.6031 (mmp) cc_final: 0.5265 (tmm) REVERT: B 661 MET cc_start: 0.8118 (tmm) cc_final: 0.7650 (tmm) REVERT: C 430 MET cc_start: 0.0999 (ptp) cc_final: -0.0227 (mmm) REVERT: C 504 MET cc_start: 0.4882 (ttt) cc_final: 0.4466 (tpp) REVERT: D 109 MET cc_start: 0.1248 (ptt) cc_final: 0.0984 (ptt) REVERT: D 329 MET cc_start: 0.4696 (tpt) cc_final: 0.3762 (mtp) REVERT: D 482 TYR cc_start: 0.1005 (p90) cc_final: 0.0263 (p90) REVERT: A 228 ILE cc_start: 0.7008 (tp) cc_final: 0.6658 (mp) REVERT: A 710 ARG cc_start: 0.8330 (mmp80) cc_final: 0.7855 (mmp80) outliers start: 3 outliers final: 0 residues processed: 286 average time/residue: 0.1720 time to fit residues: 77.2081 Evaluate side-chains 188 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 81 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 164 optimal weight: 30.0000 chunk 17 optimal weight: 0.0270 chunk 243 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 HIS D 254 HIS D 272 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.145029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.129315 restraints weight = 276191.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.128483 restraints weight = 279050.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.126708 restraints weight = 153543.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.126945 restraints weight = 151544.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.127030 restraints weight = 108697.843| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4318 r_free = 0.4318 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4318 r_free = 0.4318 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 25148 Z= 0.255 Angle : 0.775 10.462 34071 Z= 0.416 Chirality : 0.048 0.217 3868 Planarity : 0.006 0.083 4333 Dihedral : 5.623 56.895 3376 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.15 % Allowed : 3.96 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 3098 helix: 0.42 (0.13), residues: 1408 sheet: -0.64 (0.23), residues: 430 loop : -1.25 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 660 TYR 0.050 0.003 TYR D 679 PHE 0.035 0.003 PHE B 835 TRP 0.067 0.004 TRP A 709 HIS 0.007 0.001 HIS C 816 Details of bonding type rmsd covalent geometry : bond 0.00555 (25134) covalent geometry : angle 0.77461 (34043) SS BOND : bond 0.00511 ( 14) SS BOND : angle 1.47062 ( 28) hydrogen bonds : bond 0.06852 ( 1121) hydrogen bonds : angle 5.17842 ( 3257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 241 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.2600 (ptt) cc_final: 0.2188 (ptt) REVERT: B 153 MET cc_start: 0.2608 (mmm) cc_final: 0.2270 (tpp) REVERT: B 520 ILE cc_start: 0.8286 (pt) cc_final: 0.7954 (pt) REVERT: B 580 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5852 (tp) REVERT: B 661 MET cc_start: 0.8286 (tmm) cc_final: 0.7836 (tmm) REVERT: C 430 MET cc_start: 0.1982 (ptp) cc_final: 0.0157 (mmm) REVERT: C 504 MET cc_start: 0.5752 (ttt) cc_final: 0.5500 (tpp) REVERT: C 852 GLU cc_start: 0.5827 (pt0) cc_final: 0.5623 (pt0) REVERT: D 381 MET cc_start: 0.2666 (tmm) cc_final: 0.2327 (tmm) outliers start: 4 outliers final: 1 residues processed: 245 average time/residue: 0.1487 time to fit residues: 59.5529 Evaluate side-chains 171 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 115 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 185 optimal weight: 40.0000 chunk 108 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN B 786 GLN C 71 ASN D 150 ASN D 184 GLN ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.144499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.130560 restraints weight = 234758.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.127512 restraints weight = 231663.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.125695 restraints weight = 164085.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.125364 restraints weight = 158579.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.124901 restraints weight = 126911.075| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4284 r_free = 0.4284 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4284 r_free = 0.4284 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25148 Z= 0.227 Angle : 0.713 9.776 34071 Z= 0.379 Chirality : 0.046 0.266 3868 Planarity : 0.005 0.147 4333 Dihedral : 5.619 56.915 3376 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3098 helix: 0.34 (0.13), residues: 1403 sheet: -0.57 (0.24), residues: 425 loop : -1.34 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 225 TYR 0.046 0.003 TYR A 737 PHE 0.028 0.002 PHE A 705 TRP 0.060 0.003 TRP B 709 HIS 0.013 0.001 HIS C 807 Details of bonding type rmsd covalent geometry : bond 0.00492 (25134) covalent geometry : angle 0.71242 (34043) SS BOND : bond 0.00257 ( 14) SS BOND : angle 1.17625 ( 28) hydrogen bonds : bond 0.06089 ( 1121) hydrogen bonds : angle 5.07085 ( 3257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.2641 (ptt) cc_final: 0.2279 (ptt) REVERT: B 329 MET cc_start: 0.0661 (ptt) cc_final: 0.0415 (ptt) REVERT: B 365 MET cc_start: -0.0757 (mmt) cc_final: -0.1158 (ttm) REVERT: B 381 MET cc_start: 0.3500 (tpp) cc_final: 0.1161 (ttt) REVERT: B 389 ASN cc_start: 0.3574 (t0) cc_final: 0.2441 (m-40) REVERT: B 661 MET cc_start: 0.8081 (tmm) cc_final: 0.7755 (tmm) REVERT: C 409 MET cc_start: 0.6571 (ttt) cc_final: 0.5778 (ttt) REVERT: C 430 MET cc_start: 0.2728 (ptp) cc_final: 0.0586 (mmm) REVERT: C 504 MET cc_start: 0.5641 (ttt) cc_final: 0.5257 (tpp) REVERT: D 167 MET cc_start: 0.7766 (tmm) cc_final: 0.7435 (tmm) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1473 time to fit residues: 53.7332 Evaluate side-chains 163 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 304 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN C 51 ASN C 494 HIS D 163 GLN ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.140725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.126483 restraints weight = 231686.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.123379 restraints weight = 222433.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.121131 restraints weight = 171451.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.121145 restraints weight = 152963.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.120552 restraints weight = 123684.001| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4211 r_free = 0.4211 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4211 r_free = 0.4211 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 25148 Z= 0.300 Angle : 0.842 11.773 34071 Z= 0.450 Chirality : 0.049 0.256 3868 Planarity : 0.006 0.087 4333 Dihedral : 6.297 62.825 3376 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 3098 helix: -0.05 (0.13), residues: 1403 sheet: -0.64 (0.24), residues: 438 loop : -1.52 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 225 TYR 0.065 0.003 TYR D 679 PHE 0.044 0.003 PHE D 563 TRP 0.046 0.004 TRP B 709 HIS 0.007 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00656 (25134) covalent geometry : angle 0.84120 (34043) SS BOND : bond 0.00281 ( 14) SS BOND : angle 1.74368 ( 28) hydrogen bonds : bond 0.07239 ( 1121) hydrogen bonds : angle 5.70258 ( 3257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.2882 (ptt) cc_final: 0.2512 (ptt) REVERT: B 329 MET cc_start: 0.0427 (ptt) cc_final: -0.0347 (ptt) REVERT: B 381 MET cc_start: 0.3284 (tpp) cc_final: 0.1207 (ttt) REVERT: B 389 ASN cc_start: 0.3264 (t0) cc_final: 0.2641 (m-40) REVERT: C 409 MET cc_start: 0.6322 (ttt) cc_final: 0.5668 (ttt) REVERT: C 430 MET cc_start: 0.3326 (ptp) cc_final: 0.0609 (mmm) REVERT: C 504 MET cc_start: 0.6201 (ttt) cc_final: 0.5600 (tpp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1434 time to fit residues: 49.0175 Evaluate side-chains 157 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 274 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 298 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS A 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.143868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.130468 restraints weight = 207931.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.127157 restraints weight = 211180.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.125098 restraints weight = 156862.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.125203 restraints weight = 137018.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.124884 restraints weight = 101560.136| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4290 r_free = 0.4290 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4290 r_free = 0.4290 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25148 Z= 0.161 Angle : 0.649 8.039 34071 Z= 0.342 Chirality : 0.043 0.245 3868 Planarity : 0.004 0.069 4333 Dihedral : 5.657 63.799 3376 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3098 helix: 0.50 (0.14), residues: 1400 sheet: -0.58 (0.25), residues: 402 loop : -1.41 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 225 TYR 0.038 0.002 TYR D 679 PHE 0.035 0.002 PHE A 835 TRP 0.064 0.002 TRP D 162 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00350 (25134) covalent geometry : angle 0.64785 (34043) SS BOND : bond 0.00438 ( 14) SS BOND : angle 1.45014 ( 28) hydrogen bonds : bond 0.05711 ( 1121) hydrogen bonds : angle 4.99716 ( 3257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.2748 (ptt) cc_final: 0.2450 (ptt) REVERT: B 329 MET cc_start: 0.0311 (ptt) cc_final: -0.0186 (ppp) REVERT: B 365 MET cc_start: -0.0533 (mmt) cc_final: -0.1064 (ttm) REVERT: B 381 MET cc_start: 0.3305 (tpp) cc_final: 0.1364 (ttt) REVERT: B 389 ASN cc_start: 0.3119 (t0) cc_final: 0.2654 (m-40) REVERT: B 520 ILE cc_start: 0.8470 (pt) cc_final: 0.8207 (pt) REVERT: C 409 MET cc_start: 0.6280 (ttt) cc_final: 0.5886 (ttt) REVERT: C 430 MET cc_start: 0.3407 (ptp) cc_final: 0.0697 (mmm) REVERT: C 504 MET cc_start: 0.5715 (ttt) cc_final: 0.5271 (tpp) REVERT: C 673 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8018 (tptp) REVERT: C 677 MET cc_start: 0.5927 (tmm) cc_final: 0.5695 (tmm) REVERT: D 167 MET cc_start: 0.7612 (tmm) cc_final: 0.7340 (tmm) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1458 time to fit residues: 52.8033 Evaluate side-chains 168 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 110 optimal weight: 40.0000 chunk 163 optimal weight: 30.0000 chunk 114 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN C 179 GLN C 494 HIS ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.141472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.127075 restraints weight = 232606.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.125085 restraints weight = 239625.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.123643 restraints weight = 151095.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.123375 restraints weight = 143572.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.123248 restraints weight = 109488.017| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4264 r_free = 0.4264 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4264 r_free = 0.4264 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25148 Z= 0.221 Angle : 0.731 13.230 34071 Z= 0.388 Chirality : 0.045 0.255 3868 Planarity : 0.005 0.079 4333 Dihedral : 5.922 64.326 3376 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3098 helix: 0.38 (0.14), residues: 1399 sheet: -0.64 (0.26), residues: 409 loop : -1.49 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 710 TYR 0.046 0.003 TYR D 679 PHE 0.032 0.002 PHE D 563 TRP 0.061 0.003 TRP B 709 HIS 0.006 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00484 (25134) covalent geometry : angle 0.73027 (34043) SS BOND : bond 0.00225 ( 14) SS BOND : angle 1.36718 ( 28) hydrogen bonds : bond 0.06334 ( 1121) hydrogen bonds : angle 5.34709 ( 3257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.2633 (ptt) cc_final: 0.2370 (ptt) REVERT: B 365 MET cc_start: -0.0408 (mmt) cc_final: -0.0897 (ttm) REVERT: B 520 ILE cc_start: 0.8555 (pt) cc_final: 0.8334 (pt) REVERT: C 346 MET cc_start: -0.0461 (tpt) cc_final: -0.0756 (mmm) REVERT: C 409 MET cc_start: 0.6390 (ttt) cc_final: 0.6024 (ttt) REVERT: C 430 MET cc_start: 0.3562 (ptp) cc_final: 0.0730 (mmm) REVERT: C 504 MET cc_start: 0.5974 (ttt) cc_final: 0.5741 (tpp) REVERT: C 673 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8254 (tptp) REVERT: D 167 MET cc_start: 0.7655 (tmm) cc_final: 0.7358 (tmm) REVERT: D 409 MET cc_start: -0.0770 (tmm) cc_final: -0.1176 (tmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1426 time to fit residues: 50.1362 Evaluate side-chains 164 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 300 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 246 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 131 optimal weight: 0.0020 chunk 221 optimal weight: 0.2980 chunk 3 optimal weight: 30.0000 chunk 6 optimal weight: 50.0000 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 ASN D 786 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.145289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.127611 restraints weight = 206021.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.129326 restraints weight = 283174.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.129809 restraints weight = 142791.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.130531 restraints weight = 99016.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.130681 restraints weight = 86898.688| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25148 Z= 0.119 Angle : 0.611 10.196 34071 Z= 0.315 Chirality : 0.042 0.211 3868 Planarity : 0.004 0.081 4333 Dihedral : 5.272 68.571 3376 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3098 helix: 0.96 (0.14), residues: 1385 sheet: -0.40 (0.25), residues: 427 loop : -1.30 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 535 TYR 0.031 0.002 TYR D 679 PHE 0.020 0.001 PHE C 655 TRP 0.076 0.002 TRP B 709 HIS 0.004 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00251 (25134) covalent geometry : angle 0.61060 (34043) SS BOND : bond 0.00149 ( 14) SS BOND : angle 1.06500 ( 28) hydrogen bonds : bond 0.04763 ( 1121) hydrogen bonds : angle 4.73637 ( 3257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 MET cc_start: -0.0543 (mmt) cc_final: -0.0944 (ttm) REVERT: B 381 MET cc_start: 0.3203 (tpp) cc_final: 0.2977 (tpp) REVERT: C 346 MET cc_start: -0.0491 (tpt) cc_final: -0.0785 (mmm) REVERT: C 430 MET cc_start: 0.3369 (ptp) cc_final: 0.0697 (mmm) REVERT: C 655 PHE cc_start: 0.8661 (t80) cc_final: 0.8034 (t80) REVERT: C 673 LYS cc_start: 0.8301 (mmmt) cc_final: 0.8067 (tptp) REVERT: C 677 MET cc_start: 0.5365 (tmm) cc_final: 0.5055 (tmm) REVERT: D 167 MET cc_start: 0.7567 (tmm) cc_final: 0.7362 (tmm) REVERT: D 329 MET cc_start: 0.4600 (tpt) cc_final: 0.3521 (mtp) REVERT: D 409 MET cc_start: -0.0167 (tmm) cc_final: -0.0537 (tmm) REVERT: D 520 ILE cc_start: 0.8010 (pt) cc_final: 0.7810 (pt) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1461 time to fit residues: 53.3342 Evaluate side-chains 180 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 224 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 256 optimal weight: 9.9990 chunk 306 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 303 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS B 669 GLN C 299 HIS A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.130717 restraints weight = 233430.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.130018 restraints weight = 182003.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.126831 restraints weight = 132457.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.125805 restraints weight = 113526.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.124805 restraints weight = 94617.709| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25148 Z= 0.154 Angle : 0.653 11.059 34071 Z= 0.336 Chirality : 0.042 0.168 3868 Planarity : 0.004 0.065 4333 Dihedral : 5.319 63.748 3376 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3098 helix: 0.91 (0.14), residues: 1398 sheet: -0.53 (0.25), residues: 429 loop : -1.31 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 710 TYR 0.023 0.002 TYR A 737 PHE 0.022 0.002 PHE D 655 TRP 0.077 0.002 TRP B 709 HIS 0.003 0.001 HIS B 807 Details of bonding type rmsd covalent geometry : bond 0.00336 (25134) covalent geometry : angle 0.65212 (34043) SS BOND : bond 0.00171 ( 14) SS BOND : angle 1.43634 ( 28) hydrogen bonds : bond 0.05227 ( 1121) hydrogen bonds : angle 4.89843 ( 3257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: B 167 MET cc_start: 0.7169 (tmm) cc_final: 0.6272 (tmm) REVERT: B 365 MET cc_start: -0.0494 (mmt) cc_final: -0.0976 (ttm) REVERT: B 381 MET cc_start: 0.3190 (tpp) cc_final: 0.2918 (tpp) REVERT: B 668 PHE cc_start: 0.7351 (t80) cc_final: 0.7095 (t80) REVERT: C 346 MET cc_start: -0.0561 (tpt) cc_final: -0.0849 (mmm) REVERT: C 430 MET cc_start: 0.3171 (ptp) cc_final: 0.0476 (mmm) REVERT: C 673 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8197 (tptp) REVERT: C 677 MET cc_start: 0.5559 (tmm) cc_final: 0.5201 (tmm) REVERT: D 167 MET cc_start: 0.7577 (tmm) cc_final: 0.7296 (tmm) REVERT: D 409 MET cc_start: 0.0218 (tmm) cc_final: -0.0164 (tmm) REVERT: D 451 MET cc_start: 0.8255 (ppp) cc_final: 0.8040 (ppp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1375 time to fit residues: 49.3063 Evaluate side-chains 177 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 27 optimal weight: 30.0000 chunk 288 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 85 optimal weight: 30.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.143115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.125311 restraints weight = 193374.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.126340 restraints weight = 264499.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.127016 restraints weight = 148952.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.126537 restraints weight = 135603.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.127016 restraints weight = 117898.162| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4334 r_free = 0.4334 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4334 r_free = 0.4334 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25148 Z= 0.148 Angle : 0.645 10.716 34071 Z= 0.332 Chirality : 0.042 0.180 3868 Planarity : 0.004 0.062 4333 Dihedral : 5.308 66.254 3376 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3098 helix: 0.97 (0.14), residues: 1397 sheet: -0.47 (0.25), residues: 435 loop : -1.34 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 225 TYR 0.022 0.002 TYR A 737 PHE 0.039 0.002 PHE A 655 TRP 0.081 0.002 TRP B 709 HIS 0.006 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00327 (25134) covalent geometry : angle 0.64399 (34043) SS BOND : bond 0.00213 ( 14) SS BOND : angle 1.53572 ( 28) hydrogen bonds : bond 0.05133 ( 1121) hydrogen bonds : angle 4.86318 ( 3257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 MET cc_start: 0.7352 (tmm) cc_final: 0.6181 (tmm) REVERT: B 365 MET cc_start: -0.0367 (mmt) cc_final: -0.0908 (ttm) REVERT: B 381 MET cc_start: 0.3357 (tpp) cc_final: 0.3126 (tpp) REVERT: B 668 PHE cc_start: 0.7410 (t80) cc_final: 0.7088 (t80) REVERT: C 430 MET cc_start: 0.3347 (ptp) cc_final: 0.0611 (mmm) REVERT: C 673 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8121 (tptp) REVERT: C 677 MET cc_start: 0.5543 (tmm) cc_final: 0.5290 (tmm) REVERT: D 504 MET cc_start: 0.8097 (tpp) cc_final: 0.7836 (tpp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1422 time to fit residues: 51.3687 Evaluate side-chains 175 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 141 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 chunk 216 optimal weight: 0.0370 chunk 35 optimal weight: 50.0000 chunk 275 optimal weight: 0.4980 chunk 209 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.145302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.128402 restraints weight = 186913.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.130688 restraints weight = 234794.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.130927 restraints weight = 105192.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.131172 restraints weight = 81523.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.131359 restraints weight = 72719.840| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4417 r_free = 0.4417 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4417 r_free = 0.4417 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25148 Z= 0.117 Angle : 0.609 10.281 34071 Z= 0.309 Chirality : 0.041 0.172 3868 Planarity : 0.004 0.092 4333 Dihedral : 5.016 66.655 3376 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3098 helix: 1.22 (0.14), residues: 1390 sheet: -0.37 (0.25), residues: 422 loop : -1.30 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 226 TYR 0.018 0.001 TYR A 220 PHE 0.022 0.001 PHE A 655 TRP 0.083 0.002 TRP B 709 HIS 0.006 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00251 (25134) covalent geometry : angle 0.60742 (34043) SS BOND : bond 0.00126 ( 14) SS BOND : angle 1.51831 ( 28) hydrogen bonds : bond 0.04449 ( 1121) hydrogen bonds : angle 4.60869 ( 3257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4427.79 seconds wall clock time: 77 minutes 28.27 seconds (4648.27 seconds total)