Starting phenix.real_space_refine on Sun Sep 13 11:36:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.map" model { file = "/net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6whr_21673/09_2026/6whr_21673.cif" } resolution = 3.99 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= 0.015 sd= 0.684 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 130 5.16 5 C 14984 2.51 5 N 3828 2.21 5 O 4428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23370 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5870 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 539 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 22, 'HIS:plan': 7, 'GLU:plan': 17, 'GLN:plan1': 5, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5717 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 25, 'ASP:plan': 13, 'HIS:plan': 7, 'PHE:plan': 8, 'ARG:plan': 8, 'GLN:plan1': 9, 'TYR:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 343 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, D, F Time building chain proxies: 10.49, per 1000 atoms: 0.45 Number of scatterers: 23370 At special positions: 0 Unit cell: (143.85, 149.33, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 4428 8.00 N 3828 7.00 C 14984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.05 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.05 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.05 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.05 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 224 " " NAG A1002 " - " ASN A 297 " " NAG B 903 " - " ASN B 542 " " NAG B 904 " - " ASN B 341 " " NAG B 905 " - " ASN B 491 " " NAG C1001 " - " ASN C 224 " " NAG C1002 " - " ASN C 297 " " NAG D 903 " - " ASN D 542 " " NAG D 904 " - " ASN D 341 " " NAG D 905 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 808.2 milliseconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5912 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 30 sheets defined 41.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.656A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.772A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.965A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.029A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 5.176A pdb=" N MET A 155 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 157 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.668A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.694A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.514A pdb=" N ALA A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.004A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.562A pdb=" N GLU A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.982A pdb=" N TYR A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 548' Processing helix chain 'A' and resid 576 through 580 removed outlier: 4.373A pdb=" N GLN A 580 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 4.330A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.895A pdb=" N TRP A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 3.687A pdb=" N ILE A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.608A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.984A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 743 Processing helix chain 'A' and resid 754 through 764 removed outlier: 5.286A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 removed outlier: 3.517A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 removed outlier: 3.681A pdb=" N ASP A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.813A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.954A pdb=" N LYS B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 4.314A pdb=" N VAL B 64 " --> pdb=" O HIS B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.855A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.876A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.668A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.557A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 310 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.986A pdb=" N GLU B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 578 removed outlier: 3.619A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 4.311A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 654 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.849A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.549A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.637A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.805A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 839 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.657A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.773A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.964A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 143 through 148 removed outlier: 4.028A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 157 removed outlier: 5.176A pdb=" N MET C 155 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 157 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 removed outlier: 3.668A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.694A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.514A pdb=" N ALA C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 315 removed outlier: 4.004A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.563A pdb=" N GLU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 548 removed outlier: 3.981A pdb=" N TYR C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 548 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 548' Processing helix chain 'C' and resid 576 through 580 removed outlier: 4.372A pdb=" N GLN C 580 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 605 removed outlier: 4.330A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.896A pdb=" N TRP C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 3.688A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.608A pdb=" N ARG C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.983A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 743 Processing helix chain 'C' and resid 754 through 764 removed outlier: 5.287A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 801 removed outlier: 3.517A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 removed outlier: 3.682A pdb=" N ASP C 810 " --> pdb=" O MET C 806 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS C 811 " --> pdb=" O GLU C 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 812 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.813A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.954A pdb=" N LYS D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 4.314A pdb=" N VAL D 64 " --> pdb=" O HIS D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.854A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.876A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.668A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 234 through 248 removed outlier: 3.556A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 310 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.986A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.619A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 4.311A pdb=" N ILE D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 654 Processing helix chain 'D' and resid 668 through 672 Processing helix chain 'D' and resid 690 through 699 removed outlier: 3.851A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.549A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.637A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU D 793 " --> pdb=" O MET D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 843 removed outlier: 3.805A pdb=" N ALA D 828 " --> pdb=" O MET D 824 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER D 838 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU D 839 " --> pdb=" O THR D 835 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.449A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 6.445A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 166 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 7.357A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.773A pdb=" N THR A 423 " --> pdb=" O HIS A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 removed outlier: 4.433A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 753 removed outlier: 3.631A pdb=" N VAL A 563 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 768 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.631A pdb=" N ILE B 37 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 204 removed outlier: 8.097A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 280 removed outlier: 6.882A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AB3, first strand: chain 'B' and resid 475 through 477 removed outlier: 8.964A pdb=" N MET B 508 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB6, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.853A pdb=" N ALA B 728 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.448A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 removed outlier: 6.445A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 166 " --> pdb=" O SER C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 288 through 292 removed outlier: 7.356A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 422 through 423 removed outlier: 3.773A pdb=" N THR C 423 " --> pdb=" O HIS C 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 430 through 434 Processing sheet with id=AC3, first strand: chain 'C' and resid 508 through 511 removed outlier: 4.434A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 750 through 753 removed outlier: 3.631A pdb=" N VAL C 563 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 768 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.631A pdb=" N ILE D 37 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 199 through 204 removed outlier: 8.098A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 278 through 280 removed outlier: 6.882A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 341 through 344 Processing sheet with id=AC9, first strand: chain 'D' and resid 475 through 477 removed outlier: 8.964A pdb=" N MET D 508 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER D 407 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 419 through 420 Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.854A pdb=" N ALA D 728 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2658 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: 3.37 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6131 1.33 - 1.46: 6905 1.46 - 1.59: 10604 1.59 - 1.72: 0 1.72 - 1.85: 218 Bond restraints: 23858 Sorted by residual: bond pdb=" CA ALA A 755 " pdb=" C ALA A 755 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.79e+01 bond pdb=" CA ALA C 755 " pdb=" C ALA C 755 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.75e+01 bond pdb=" CA SER D 520 " pdb=" C SER D 520 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.34e-02 5.57e+03 4.43e+01 bond pdb=" CA SER B 520 " pdb=" C SER B 520 " ideal model delta sigma weight residual 1.523 1.435 0.089 1.34e-02 5.57e+03 4.37e+01 bond pdb=" CA MET B 789 " pdb=" C MET B 789 " ideal model delta sigma weight residual 1.524 1.404 0.120 2.25e-02 1.98e+03 2.83e+01 ... (remaining 23853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 31154 2.66 - 5.32: 1248 5.32 - 7.97: 121 7.97 - 10.63: 49 10.63 - 13.29: 14 Bond angle restraints: 32586 Sorted by residual: angle pdb=" C LYS D 747 " pdb=" N LEU D 748 " pdb=" CA LEU D 748 " ideal model delta sigma weight residual 121.64 114.05 7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" C LYS B 747 " pdb=" N LEU B 748 " pdb=" CA LEU B 748 " ideal model delta sigma weight residual 121.64 114.09 7.55 1.20e+00 6.94e-01 3.96e+01 angle pdb=" C PHE D 529 " pdb=" CA PHE D 529 " pdb=" CB PHE D 529 " ideal model delta sigma weight residual 111.39 103.02 8.37 1.59e+00 3.96e-01 2.77e+01 angle pdb=" C PHE B 529 " pdb=" CA PHE B 529 " pdb=" CB PHE B 529 " ideal model delta sigma weight residual 111.39 103.07 8.32 1.59e+00 3.96e-01 2.73e+01 angle pdb=" C LEU C 676 " pdb=" N VAL C 677 " pdb=" CA VAL C 677 " ideal model delta sigma weight residual 122.35 116.84 5.51 1.18e+00 7.18e-01 2.18e+01 ... (remaining 32581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 12390 17.03 - 34.07: 1233 34.07 - 51.10: 265 51.10 - 68.13: 60 68.13 - 85.16: 14 Dihedral angle restraints: 13962 sinusoidal: 4802 harmonic: 9160 Sorted by residual: dihedral pdb=" CA CYS D 429 " pdb=" C CYS D 429 " pdb=" N MET D 430 " pdb=" CA MET D 430 " ideal model delta harmonic sigma weight residual 180.00 132.00 48.00 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA CYS B 429 " pdb=" C CYS B 429 " pdb=" N MET B 430 " pdb=" CA MET B 430 " ideal model delta harmonic sigma weight residual 180.00 132.06 47.94 0 5.00e+00 4.00e-02 9.19e+01 dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -165.58 79.58 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 13959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3910 0.321 - 0.643: 2 0.643 - 0.964: 0 0.964 - 1.286: 0 1.286 - 1.607: 2 Chirality restraints: 3914 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.79 -1.61 2.00e-02 2.50e+03 6.46e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.79 -1.61 2.00e-02 2.50e+03 6.45e+03 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 224 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.03e+00 ... (remaining 3911 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 632 " -0.023 2.00e-02 2.50e+03 1.52e-02 5.81e+00 pdb=" CG TRP A 632 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 632 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 632 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 632 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 632 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 632 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 632 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 632 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 632 " 0.023 2.00e-02 2.50e+03 1.52e-02 5.81e+00 pdb=" CG TRP C 632 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 632 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 632 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 632 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 632 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 632 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 632 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 632 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 547 " 0.001 2.00e-02 2.50e+03 1.61e-02 5.17e+00 pdb=" CG TYR C 547 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 547 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 547 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 547 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 547 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 547 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 547 " -0.003 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 497 2.55 - 3.14: 24171 3.14 - 3.73: 35745 3.73 - 4.31: 46420 4.31 - 4.90: 70640 Nonbonded interactions: 177473 Sorted by model distance: nonbonded pdb=" OG1 THR A 446 " pdb=" OD1 ASN A 448 " model vdw 1.968 3.040 nonbonded pdb=" OG1 THR C 446 " pdb=" OD1 ASN C 448 " model vdw 1.968 3.040 nonbonded pdb=" O LYS A 706 " pdb=" OG SER A 708 " model vdw 2.049 3.040 nonbonded pdb=" O LYS C 706 " pdb=" OG SER C 708 " model vdw 2.049 3.040 nonbonded pdb=" N ASP C 753 " pdb=" OD1 ASP C 753 " model vdw 2.050 3.120 ... (remaining 177468 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.000 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 : 0.015 0.120 23888 Z= 0.711 Angle : 1.367 52.976 32660 Z= 0.691 Chirality : 0.071 1.607 3914 Planarity : 0.006 0.053 4132 Dihedral : 14.891 85.163 8002 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 30.76 Ramachandran Plot: Outliers : 0.83 % Allowed : 21.19 % Favored : 77.98 % Rotamer: Outliers : 2.94 % Allowed : 16.88 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.90 (0.11), residues: 3138 helix: -3.34 (0.11), residues: 1132 sheet: -4.08 (0.19), residues: 370 loop : -4.43 (0.12), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 544 TYR 0.034 0.003 TYR C 547 PHE 0.031 0.004 PHE B 729 TRP 0.041 0.003 TRP A 632 HIS 0.017 0.004 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.01515 / 0.71 (23858) covalent geometry : angle 1.22781 / 0.66 (32586) SS BOND : bond 0.01056 / 0.70 ( 16) SS BOND : angle 2.39291 / 1.65 ( 32) hydrogen bonds : bond 0.17549 / 11.96 ( 926) hydrogen bonds : angle 8.87769 / 6.29 ( 2658) link_BETA1-4 : bond 0.06083 / 3.05 ( 2) link_BETA1-4 : angle 42.80298 / 21.20 ( 6) link_NAG-ASN : bond 0.00956 / 0.53 ( 12) link_NAG-ASN : angle 4.54484 / 3.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7128 (t80) REVERT: A 605 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7567 (t) REVERT: A 662 MET cc_start: 0.8307 (tmm) cc_final: 0.8019 (tmm) REVERT: A 686 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8104 (p) REVERT: B 548 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.7576 (p) REVERT: B 818 MET cc_start: 0.6837 (mmm) cc_final: 0.6215 (mmp) REVERT: C 349 SER cc_start: 0.6011 (OUTLIER) cc_final: 0.5720 (p) REVERT: C 575 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7247 (t80) REVERT: C 605 SER cc_start: 0.7479 (OUTLIER) cc_final: 0.6821 (t) REVERT: C 686 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (p) REVERT: D 654 MET cc_start: 0.7862 (mmt) cc_final: 0.7612 (tpp) REVERT: D 818 MET cc_start: 0.6846 (mmm) cc_final: 0.6166 (mmt) outliers start: 68 outliers final: 47 residues processed: 262 average time/residue: 0.1167 time to fit residues: 53.7886 Evaluate side-chains 226 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 483 ASN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 760 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN A 577 GLN A 731 ASN A 748 HIS B 152 GLN B 486 HIS C 384 GLN C 577 GLN C 748 HIS D 152 GLN D 486 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064250 restraints weight = 93502.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063501 restraints weight = 65890.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063802 restraints weight = 56422.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064061 restraints weight = 50845.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.065067 restraints weight = 44116.008| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23888 Z= 0.185 Angle : 0.773 13.434 32660 Z= 0.399 Chirality : 0.048 0.450 3914 Planarity : 0.005 0.059 4132 Dihedral : 7.929 58.886 3400 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.50 % Favored : 90.41 % Rotamer: Outliers : 4.02 % Allowed : 18.52 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.13), residues: 3138 helix: -1.45 (0.13), residues: 1182 sheet: -3.31 (0.21), residues: 380 loop : -3.61 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 651 TYR 0.028 0.002 TYR A 547 PHE 0.047 0.002 PHE C 42 TRP 0.017 0.001 TRP D 607 HIS 0.010 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (23858) covalent geometry : angle 0.75719 / 0.40 (32586) SS BOND : bond 0.00865 / 0.60 ( 16) SS BOND : angle 1.92161 / 1.47 ( 32) hydrogen bonds : bond 0.05960 / 4.04 ( 926) hydrogen bonds : angle 5.82086 / 4.10 ( 2658) link_BETA1-4 : bond 0.01672 / 0.83 ( 2) link_BETA1-4 : angle 5.69813 / 3.19 ( 6) link_NAG-ASN : bond 0.00760 / 0.33 ( 12) link_NAG-ASN : angle 3.85234 / 3.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 219 time to evaluate : 0.791 Fit side-chains REVERT: A 74 MET cc_start: 0.8284 (mmm) cc_final: 0.7999 (mmm) REVERT: A 436 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: A 530 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8664 (mp10) REVERT: A 575 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7647 (t80) REVERT: A 662 MET cc_start: 0.9315 (tmm) cc_final: 0.8870 (tmm) REVERT: B 142 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8359 (ptt) REVERT: B 339 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 548 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8447 (p) REVERT: B 565 MET cc_start: 0.9077 (mmm) cc_final: 0.8695 (mmm) REVERT: B 654 MET cc_start: 0.8476 (mmp) cc_final: 0.8128 (mmt) REVERT: B 790 GLU cc_start: 0.7976 (tp30) cc_final: 0.7600 (tp30) REVERT: B 797 LEU cc_start: 0.9225 (mt) cc_final: 0.8934 (mp) REVERT: C 74 MET cc_start: 0.8243 (mmm) cc_final: 0.7864 (mmm) REVERT: C 125 MET cc_start: 0.9301 (mmm) cc_final: 0.8673 (mmm) REVERT: C 530 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: C 575 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7862 (t80) REVERT: C 662 MET cc_start: 0.9236 (tmm) cc_final: 0.9029 (tmm) REVERT: C 712 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8961 (tt) REVERT: D 142 MET cc_start: 0.8409 (ptp) cc_final: 0.7874 (ptp) REVERT: D 339 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8528 (mm) REVERT: D 385 GLN cc_start: 0.6912 (mt0) cc_final: 0.6637 (pt0) REVERT: D 562 MET cc_start: 0.8454 (tmm) cc_final: 0.8186 (tmm) REVERT: D 788 GLU cc_start: 0.8498 (mp0) cc_final: 0.8172 (mp0) outliers start: 93 outliers final: 56 residues processed: 304 average time/residue: 0.1222 time to fit residues: 65.0168 Evaluate side-chains 254 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 230 optimal weight: 0.8980 chunk 257 optimal weight: 30.0000 chunk 271 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 138 optimal weight: 0.0670 chunk 105 optimal weight: 8.9990 chunk 294 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 801 HIS C 731 ASN C 801 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.087904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066018 restraints weight = 92060.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065863 restraints weight = 61224.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066456 restraints weight = 47663.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066761 restraints weight = 41703.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067067 restraints weight = 37985.946| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23888 Z= 0.136 Angle : 0.683 12.434 32660 Z= 0.349 Chirality : 0.046 0.407 3914 Planarity : 0.004 0.058 4132 Dihedral : 6.892 59.575 3365 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 4.32 % Allowed : 19.60 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.14), residues: 3138 helix: -0.22 (0.15), residues: 1198 sheet: -2.86 (0.24), residues: 356 loop : -3.15 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 725 TYR 0.019 0.001 TYR C 109 PHE 0.014 0.001 PHE B 757 TRP 0.017 0.001 TRP A 519 HIS 0.008 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (23858) covalent geometry : angle 0.66757 / 0.35 (32586) SS BOND : bond 0.00578 / 0.40 ( 16) SS BOND : angle 1.51040 / 1.09 ( 32) hydrogen bonds : bond 0.04552 / 3.11 ( 926) hydrogen bonds : angle 5.12539 / 3.63 ( 2658) link_BETA1-4 : bond 0.01947 / 0.98 ( 2) link_BETA1-4 : angle 5.64800 / 3.16 ( 6) link_NAG-ASN : bond 0.00792 / 0.35 ( 12) link_NAG-ASN : angle 3.57649 / 2.96 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 215 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8478 (p90) REVERT: A 74 MET cc_start: 0.8292 (mmm) cc_final: 0.7842 (mmm) REVERT: A 125 MET cc_start: 0.9405 (mmm) cc_final: 0.9204 (mmm) REVERT: A 261 MET cc_start: 0.8790 (tpp) cc_final: 0.8136 (tpp) REVERT: A 351 TYR cc_start: 0.7006 (t80) cc_final: 0.6762 (t80) REVERT: A 436 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7957 (mpp) REVERT: A 575 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 662 MET cc_start: 0.9499 (tmm) cc_final: 0.9144 (tmm) REVERT: A 789 TRP cc_start: 0.8225 (OUTLIER) cc_final: 0.6547 (p-90) REVERT: B 334 MET cc_start: 0.8381 (mmp) cc_final: 0.8060 (pmm) REVERT: B 339 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8384 (mm) REVERT: B 562 MET cc_start: 0.8349 (tmm) cc_final: 0.7899 (tmm) REVERT: B 565 MET cc_start: 0.9035 (mmm) cc_final: 0.8787 (mmm) REVERT: B 654 MET cc_start: 0.8292 (mmp) cc_final: 0.8082 (tpp) REVERT: B 797 LEU cc_start: 0.9251 (mt) cc_final: 0.9047 (mp) REVERT: C 74 MET cc_start: 0.8267 (mmm) cc_final: 0.7798 (mmm) REVERT: C 125 MET cc_start: 0.9431 (mmm) cc_final: 0.9064 (mmm) REVERT: C 575 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7837 (t80) REVERT: C 662 MET cc_start: 0.9471 (tmm) cc_final: 0.9173 (tmm) REVERT: C 789 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.6681 (p-90) REVERT: D 142 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7806 (ptp) REVERT: D 334 MET cc_start: 0.8524 (mmp) cc_final: 0.8231 (pmm) REVERT: D 339 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (mm) outliers start: 100 outliers final: 53 residues processed: 299 average time/residue: 0.1232 time to fit residues: 63.7814 Evaluate side-chains 259 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 197 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 784 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 242 optimal weight: 20.0000 chunk 311 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 234 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 291 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068006 restraints weight = 92390.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067473 restraints weight = 59824.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067986 restraints weight = 54734.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068302 restraints weight = 45618.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068415 restraints weight = 42235.701| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23888 Z= 0.150 Angle : 0.691 12.232 32660 Z= 0.351 Chirality : 0.046 0.416 3914 Planarity : 0.004 0.053 4132 Dihedral : 6.494 58.889 3352 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.67 % Favored : 91.27 % Rotamer: Outliers : 4.49 % Allowed : 20.25 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 3138 helix: 0.12 (0.15), residues: 1204 sheet: -2.67 (0.24), residues: 360 loop : -3.06 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 712 TYR 0.019 0.001 TYR A 109 PHE 0.015 0.001 PHE D 677 TRP 0.012 0.001 TRP D 635 HIS 0.018 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (23858) covalent geometry : angle 0.67418 / 0.35 (32586) SS BOND : bond 0.00527 / 0.38 ( 16) SS BOND : angle 2.37517 / 1.83 ( 32) hydrogen bonds : bond 0.04357 / 2.98 ( 926) hydrogen bonds : angle 5.02133 / 3.55 ( 2658) link_BETA1-4 : bond 0.01859 / 0.94 ( 2) link_BETA1-4 : angle 5.37496 / 3.01 ( 6) link_NAG-ASN : bond 0.00748 / 0.33 ( 12) link_NAG-ASN : angle 3.53103 / 2.91 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 197 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8321 (p90) REVERT: A 74 MET cc_start: 0.8350 (mmm) cc_final: 0.7832 (mmm) REVERT: A 290 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5655 (pp) REVERT: A 436 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7991 (mpp) REVERT: A 530 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8515 (mp10) REVERT: A 575 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7484 (t80) REVERT: A 662 MET cc_start: 0.9478 (tmm) cc_final: 0.9092 (tmm) REVERT: A 789 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.6631 (p-90) REVERT: B 307 MET cc_start: 0.5228 (ppp) cc_final: 0.5011 (ppp) REVERT: B 334 MET cc_start: 0.8420 (mmp) cc_final: 0.7882 (pmm) REVERT: B 339 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8356 (mm) REVERT: B 565 MET cc_start: 0.9046 (mmm) cc_final: 0.8798 (mmm) REVERT: B 797 LEU cc_start: 0.9259 (mt) cc_final: 0.9044 (mp) REVERT: C 74 MET cc_start: 0.8295 (mmm) cc_final: 0.7848 (mmm) REVERT: C 125 MET cc_start: 0.9471 (mmm) cc_final: 0.9161 (mmm) REVERT: C 530 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: C 575 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7746 (t80) REVERT: C 662 MET cc_start: 0.9442 (tmm) cc_final: 0.9099 (tmm) REVERT: C 727 MET cc_start: 0.8380 (ptm) cc_final: 0.8092 (ppp) REVERT: C 789 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.6775 (p-90) REVERT: D 142 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7818 (ptp) REVERT: D 334 MET cc_start: 0.8648 (mmp) cc_final: 0.8258 (pmm) REVERT: D 339 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8465 (mm) outliers start: 104 outliers final: 78 residues processed: 285 average time/residue: 0.1236 time to fit residues: 62.2103 Evaluate side-chains 284 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 194 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 784 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 249 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN ** C 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.091582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069518 restraints weight = 91327.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.069291 restraints weight = 55971.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069817 restraints weight = 51457.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070246 restraints weight = 42979.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070394 restraints weight = 39075.510| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23888 Z= 0.116 Angle : 0.651 11.655 32660 Z= 0.328 Chirality : 0.045 0.391 3914 Planarity : 0.004 0.051 4132 Dihedral : 6.049 59.844 3350 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.38 % Rotamer: Outliers : 4.79 % Allowed : 19.78 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.15), residues: 3138 helix: 0.42 (0.15), residues: 1222 sheet: -2.37 (0.24), residues: 388 loop : -2.94 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 712 TYR 0.019 0.001 TYR C 109 PHE 0.014 0.001 PHE C 493 TRP 0.010 0.001 TRP D 607 HIS 0.007 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (23858) covalent geometry : angle 0.63647 / 0.32 (32586) SS BOND : bond 0.00473 / 0.33 ( 16) SS BOND : angle 1.96230 / 1.52 ( 32) hydrogen bonds : bond 0.03770 / 2.59 ( 926) hydrogen bonds : angle 4.75493 / 3.37 ( 2658) link_BETA1-4 : bond 0.01843 / 0.93 ( 2) link_BETA1-4 : angle 4.40293 / 2.47 ( 6) link_NAG-ASN : bond 0.00741 / 0.32 ( 12) link_NAG-ASN : angle 3.36208 / 2.78 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 217 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8735 (mpp) cc_final: 0.8438 (ppp) REVERT: A 42 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8279 (p90) REVERT: A 74 MET cc_start: 0.8349 (mmm) cc_final: 0.7860 (mmm) REVERT: A 436 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7969 (mpp) REVERT: A 530 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: A 575 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7358 (t80) REVERT: A 662 MET cc_start: 0.9505 (tmm) cc_final: 0.9191 (tmm) REVERT: A 700 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7730 (t80) REVERT: A 789 TRP cc_start: 0.8294 (OUTLIER) cc_final: 0.6716 (p-90) REVERT: A 831 CYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6843 (m) REVERT: B 157 MET cc_start: 0.8493 (ptt) cc_final: 0.8226 (ppp) REVERT: B 334 MET cc_start: 0.8338 (mmp) cc_final: 0.7931 (pmm) REVERT: B 339 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 562 MET cc_start: 0.8267 (tmm) cc_final: 0.8037 (ppp) REVERT: B 565 MET cc_start: 0.8997 (mmm) cc_final: 0.8612 (mmm) REVERT: B 748 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5149 (mt) REVERT: B 797 LEU cc_start: 0.9228 (mt) cc_final: 0.9020 (mp) REVERT: C 42 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8422 (p90) REVERT: C 74 MET cc_start: 0.8279 (mmm) cc_final: 0.7845 (mmm) REVERT: C 125 MET cc_start: 0.9451 (mmm) cc_final: 0.9117 (mmm) REVERT: C 491 MET cc_start: 0.8839 (mmm) cc_final: 0.8627 (mmt) REVERT: C 530 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: C 575 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7558 (t80) REVERT: C 662 MET cc_start: 0.9471 (tmm) cc_final: 0.9088 (tmm) REVERT: C 700 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7708 (t80) REVERT: C 727 MET cc_start: 0.8368 (ptm) cc_final: 0.8024 (ppp) REVERT: C 789 TRP cc_start: 0.8317 (OUTLIER) cc_final: 0.6801 (p-90) REVERT: D 142 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7847 (ptp) REVERT: D 334 MET cc_start: 0.8598 (mmp) cc_final: 0.8149 (pmm) REVERT: D 339 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8455 (mm) REVERT: D 562 MET cc_start: 0.8522 (tmm) cc_final: 0.8219 (tmm) outliers start: 111 outliers final: 72 residues processed: 311 average time/residue: 0.1195 time to fit residues: 65.6387 Evaluate side-chains 286 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 198 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 273 optimal weight: 0.7980 chunk 97 optimal weight: 0.0470 chunk 210 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 239 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 237 optimal weight: 30.0000 chunk 146 optimal weight: 0.5980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 HIS C 801 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.092653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071198 restraints weight = 91545.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070017 restraints weight = 63320.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070738 restraints weight = 52351.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071135 restraints weight = 44297.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071341 restraints weight = 40006.896| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23888 Z= 0.111 Angle : 0.644 11.329 32660 Z= 0.324 Chirality : 0.044 0.385 3914 Planarity : 0.004 0.047 4132 Dihedral : 5.733 58.350 3350 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.53 % Allowed : 20.51 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.15), residues: 3138 helix: 0.63 (0.15), residues: 1218 sheet: -2.29 (0.24), residues: 392 loop : -2.79 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 712 TYR 0.018 0.001 TYR A 109 PHE 0.022 0.001 PHE B 677 TRP 0.008 0.001 TRP D 607 HIS 0.005 0.000 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23858) covalent geometry : angle 0.63174 / 0.32 (32586) SS BOND : bond 0.00449 / 0.31 ( 16) SS BOND : angle 1.59096 / 1.22 ( 32) hydrogen bonds : bond 0.03465 / 2.38 ( 926) hydrogen bonds : angle 4.56769 / 3.24 ( 2658) link_BETA1-4 : bond 0.01659 / 0.84 ( 2) link_BETA1-4 : angle 3.88709 / 2.17 ( 6) link_NAG-ASN : bond 0.00723 / 0.32 ( 12) link_NAG-ASN : angle 3.26792 / 2.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 219 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8340 (mmm) cc_final: 0.7857 (mmm) REVERT: A 154 MET cc_start: 0.8686 (mmm) cc_final: 0.8074 (mmm) REVERT: A 177 GLN cc_start: 0.9387 (tt0) cc_final: 0.9144 (tt0) REVERT: A 436 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8113 (mpp) REVERT: A 530 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8587 (mp10) REVERT: A 575 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7145 (t80) REVERT: A 662 MET cc_start: 0.9467 (tmm) cc_final: 0.9181 (tmm) REVERT: A 700 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 789 TRP cc_start: 0.8214 (OUTLIER) cc_final: 0.6737 (p-90) REVERT: A 831 CYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6881 (m) REVERT: B 171 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 227 ILE cc_start: 0.8147 (mm) cc_final: 0.7925 (mm) REVERT: B 334 MET cc_start: 0.8343 (mmp) cc_final: 0.7976 (pmm) REVERT: B 339 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8332 (mm) REVERT: B 565 MET cc_start: 0.9063 (mmm) cc_final: 0.8629 (mmm) REVERT: C 42 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8383 (p90) REVERT: C 74 MET cc_start: 0.8288 (mmm) cc_final: 0.7823 (mmm) REVERT: C 154 MET cc_start: 0.8702 (mmm) cc_final: 0.8223 (mmm) REVERT: C 530 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: C 575 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7440 (t80) REVERT: C 662 MET cc_start: 0.9450 (tmm) cc_final: 0.9126 (tmm) REVERT: C 700 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7618 (t80) REVERT: C 789 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.6729 (p-90) REVERT: D 142 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7876 (ptp) REVERT: D 171 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8222 (mm) REVERT: D 334 MET cc_start: 0.8602 (mmp) cc_final: 0.8276 (pmm) REVERT: D 339 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8462 (mm) REVERT: D 562 MET cc_start: 0.8479 (tmm) cc_final: 0.8167 (tmm) outliers start: 105 outliers final: 71 residues processed: 307 average time/residue: 0.1240 time to fit residues: 67.0547 Evaluate side-chains 291 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 204 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 457 CYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 784 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 297 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 176 optimal weight: 0.0020 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 310 optimal weight: 30.0000 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN C 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.091852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070056 restraints weight = 92522.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069331 restraints weight = 60398.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069828 restraints weight = 51854.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070317 restraints weight = 44959.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070357 restraints weight = 39939.930| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23888 Z= 0.126 Angle : 0.648 12.704 32660 Z= 0.325 Chirality : 0.044 0.388 3914 Planarity : 0.004 0.048 4132 Dihedral : 5.589 57.221 3346 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.45 % Allowed : 21.16 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.15), residues: 3138 helix: 0.74 (0.15), residues: 1214 sheet: -2.33 (0.24), residues: 388 loop : -2.65 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 712 TYR 0.019 0.001 TYR C 109 PHE 0.022 0.001 PHE B 677 TRP 0.011 0.001 TRP D 635 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (23858) covalent geometry : angle 0.63548 / 0.32 (32586) SS BOND : bond 0.00452 / 0.31 ( 16) SS BOND : angle 1.62263 / 1.22 ( 32) hydrogen bonds : bond 0.03569 / 2.44 ( 926) hydrogen bonds : angle 4.58265 / 3.24 ( 2658) link_BETA1-4 : bond 0.01631 / 0.81 ( 2) link_BETA1-4 : angle 3.62183 / 2.03 ( 6) link_NAG-ASN : bond 0.00694 / 0.30 ( 12) link_NAG-ASN : angle 3.21980 / 2.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 206 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8698 (mpp) cc_final: 0.8333 (ppp) REVERT: A 42 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8143 (p90) REVERT: A 74 MET cc_start: 0.8263 (mmm) cc_final: 0.7806 (mmm) REVERT: A 154 MET cc_start: 0.8659 (mmm) cc_final: 0.8133 (mmm) REVERT: A 177 GLN cc_start: 0.9335 (tt0) cc_final: 0.9123 (tt0) REVERT: A 436 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8212 (mpp) REVERT: A 530 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: A 549 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: A 575 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7296 (t80) REVERT: A 662 MET cc_start: 0.9377 (tmm) cc_final: 0.9091 (tmm) REVERT: A 700 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7701 (t80) REVERT: A 789 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.6791 (p-90) REVERT: A 831 CYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6756 (m) REVERT: B 171 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8523 (mm) REVERT: B 227 ILE cc_start: 0.8225 (mm) cc_final: 0.8003 (mm) REVERT: B 334 MET cc_start: 0.8285 (mmp) cc_final: 0.7963 (pmm) REVERT: B 339 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8401 (mm) REVERT: B 565 MET cc_start: 0.9037 (mmm) cc_final: 0.8645 (mmm) REVERT: C 42 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8516 (p90) REVERT: C 74 MET cc_start: 0.8210 (mmm) cc_final: 0.7768 (mmm) REVERT: C 530 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: C 549 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: C 575 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7604 (t80) REVERT: C 662 MET cc_start: 0.9375 (tmm) cc_final: 0.9050 (tmm) REVERT: C 789 TRP cc_start: 0.8246 (OUTLIER) cc_final: 0.6674 (p-90) REVERT: D 142 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7923 (ptp) REVERT: D 171 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8277 (mm) REVERT: D 334 MET cc_start: 0.8502 (mmp) cc_final: 0.8249 (pmm) REVERT: D 339 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8516 (mm) REVERT: D 562 MET cc_start: 0.8456 (tmm) cc_final: 0.8098 (tmm) outliers start: 103 outliers final: 76 residues processed: 293 average time/residue: 0.1178 time to fit residues: 60.9167 Evaluate side-chains 293 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 199 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 457 CYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 273 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 280 optimal weight: 8.9990 chunk 226 optimal weight: 0.9990 chunk 81 optimal weight: 50.0000 chunk 245 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 801 HIS C 147 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS D 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.092797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070267 restraints weight = 91575.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069839 restraints weight = 63244.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070427 restraints weight = 49290.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070821 restraints weight = 42780.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070961 restraints weight = 38821.990| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23888 Z= 0.110 Angle : 0.635 11.835 32660 Z= 0.317 Chirality : 0.044 0.375 3914 Planarity : 0.004 0.046 4132 Dihedral : 5.377 55.821 3344 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.58 % Allowed : 21.11 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 3138 helix: 0.80 (0.15), residues: 1218 sheet: -2.24 (0.24), residues: 394 loop : -2.47 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 673 TYR 0.019 0.001 TYR C 109 PHE 0.019 0.001 PHE A 850 TRP 0.011 0.001 TRP D 607 HIS 0.004 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (23858) covalent geometry : angle 0.62395 / 0.31 (32586) SS BOND : bond 0.00424 / 0.30 ( 16) SS BOND : angle 1.49692 / 1.12 ( 32) hydrogen bonds : bond 0.03400 / 2.33 ( 926) hydrogen bonds : angle 4.49033 / 3.19 ( 2658) link_BETA1-4 : bond 0.01476 / 0.74 ( 2) link_BETA1-4 : angle 3.07380 / 1.72 ( 6) link_NAG-ASN : bond 0.00687 / 0.30 ( 12) link_NAG-ASN : angle 3.13597 / 2.60 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 209 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8671 (mpp) cc_final: 0.8356 (ppp) REVERT: A 42 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8140 (p90) REVERT: A 74 MET cc_start: 0.8267 (mmm) cc_final: 0.7758 (mmm) REVERT: A 154 MET cc_start: 0.8634 (mmm) cc_final: 0.8109 (mmm) REVERT: A 436 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8221 (mpp) REVERT: A 530 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: A 549 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: A 575 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 662 MET cc_start: 0.9398 (tmm) cc_final: 0.9121 (tmm) REVERT: A 789 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.6733 (p-90) REVERT: A 831 CYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6963 (m) REVERT: B 157 MET cc_start: 0.8547 (ptt) cc_final: 0.8023 (ppp) REVERT: B 171 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8482 (mm) REVERT: B 227 ILE cc_start: 0.8178 (mm) cc_final: 0.7955 (mm) REVERT: B 334 MET cc_start: 0.8335 (mmp) cc_final: 0.7769 (pmm) REVERT: B 339 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 565 MET cc_start: 0.9018 (mmm) cc_final: 0.8638 (mmm) REVERT: C 42 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8533 (p90) REVERT: C 74 MET cc_start: 0.8244 (mmm) cc_final: 0.7700 (mmm) REVERT: C 154 MET cc_start: 0.8608 (mmm) cc_final: 0.7959 (mmm) REVERT: C 530 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8504 (mp10) REVERT: C 575 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7587 (t80) REVERT: C 662 MET cc_start: 0.9414 (tmm) cc_final: 0.9082 (tmm) REVERT: C 789 TRP cc_start: 0.8155 (OUTLIER) cc_final: 0.6637 (p-90) REVERT: C 831 CYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6857 (m) REVERT: D 142 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7910 (ptp) REVERT: D 171 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8403 (mm) REVERT: D 334 MET cc_start: 0.8535 (mmp) cc_final: 0.8248 (pmm) REVERT: D 339 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8511 (mm) REVERT: D 562 MET cc_start: 0.8463 (tmm) cc_final: 0.8260 (tmm) REVERT: D 746 CYS cc_start: 0.6709 (p) cc_final: 0.6409 (p) outliers start: 106 outliers final: 82 residues processed: 297 average time/residue: 0.1235 time to fit residues: 64.3254 Evaluate side-chains 296 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 197 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 457 CYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 44 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 170 optimal weight: 0.4980 chunk 101 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 206 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 177 GLN A 801 HIS C 147 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS D 616 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070620 restraints weight = 92284.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070018 restraints weight = 62538.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070730 restraints weight = 49943.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070973 restraints weight = 45802.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071241 restraints weight = 39477.732| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23888 Z= 0.110 Angle : 0.641 10.824 32660 Z= 0.318 Chirality : 0.044 0.373 3914 Planarity : 0.004 0.044 4132 Dihedral : 5.297 54.964 3342 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.53 % Allowed : 21.37 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.63 (0.15), residues: 3138 helix: 0.78 (0.15), residues: 1220 sheet: -2.16 (0.24), residues: 394 loop : -2.43 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 179 TYR 0.018 0.001 TYR C 109 PHE 0.017 0.001 PHE A 850 TRP 0.010 0.001 TRP D 607 HIS 0.007 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (23858) covalent geometry : angle 0.63070 / 0.32 (32586) SS BOND : bond 0.00386 / 0.27 ( 16) SS BOND : angle 1.45847 / 1.11 ( 32) hydrogen bonds : bond 0.03340 / 2.29 ( 926) hydrogen bonds : angle 4.46979 / 3.18 ( 2658) link_BETA1-4 : bond 0.01425 / 0.72 ( 2) link_BETA1-4 : angle 2.90381 / 1.62 ( 6) link_NAG-ASN : bond 0.00681 / 0.30 ( 12) link_NAG-ASN : angle 3.09643 / 2.57 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 209 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8665 (mpp) cc_final: 0.8376 (ppp) REVERT: A 42 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8165 (p90) REVERT: A 74 MET cc_start: 0.8331 (mmm) cc_final: 0.7840 (mmm) REVERT: A 154 MET cc_start: 0.8625 (mmm) cc_final: 0.8094 (mmm) REVERT: A 436 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8190 (mpp) REVERT: A 530 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8531 (mp10) REVERT: A 549 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 575 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 662 MET cc_start: 0.9401 (tmm) cc_final: 0.9129 (tmm) REVERT: A 789 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.6673 (p-90) REVERT: A 831 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6961 (m) REVERT: B 157 MET cc_start: 0.8558 (ptt) cc_final: 0.7968 (ppp) REVERT: B 171 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8470 (mm) REVERT: B 227 ILE cc_start: 0.8119 (mm) cc_final: 0.7887 (mm) REVERT: B 334 MET cc_start: 0.8375 (mmp) cc_final: 0.7766 (pmm) REVERT: B 339 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 565 MET cc_start: 0.9061 (mmm) cc_final: 0.8639 (mmm) REVERT: C 42 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8531 (p90) REVERT: C 74 MET cc_start: 0.8245 (mmm) cc_final: 0.7696 (mmm) REVERT: C 154 MET cc_start: 0.8609 (mmm) cc_final: 0.7984 (mmm) REVERT: C 530 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8504 (mp10) REVERT: C 575 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7570 (t80) REVERT: C 662 MET cc_start: 0.9409 (tmm) cc_final: 0.9081 (tmm) REVERT: C 789 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.6766 (p-90) REVERT: C 831 CYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6878 (m) REVERT: D 142 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7894 (ptp) REVERT: D 171 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 334 MET cc_start: 0.8534 (mmp) cc_final: 0.8244 (pmm) REVERT: D 339 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8508 (mm) REVERT: D 562 MET cc_start: 0.8601 (tmm) cc_final: 0.8258 (tmm) REVERT: D 654 MET cc_start: 0.8134 (tpp) cc_final: 0.7685 (ttm) REVERT: D 746 CYS cc_start: 0.6698 (p) cc_final: 0.6457 (p) outliers start: 105 outliers final: 76 residues processed: 299 average time/residue: 0.1160 time to fit residues: 61.1989 Evaluate side-chains 295 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 202 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 457 CYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 111 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 0.0670 chunk 282 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 overall best weight: 0.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 801 HIS B 152 GLN C 147 GLN C 177 GLN D 616 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.093663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071451 restraints weight = 91928.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071035 restraints weight = 58154.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071615 restraints weight = 48791.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071930 restraints weight = 42662.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072169 restraints weight = 38601.589| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23888 Z= 0.109 Angle : 0.650 12.246 32660 Z= 0.321 Chirality : 0.044 0.366 3914 Planarity : 0.004 0.043 4132 Dihedral : 5.229 54.300 3342 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.02 % Allowed : 21.93 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.54 (0.15), residues: 3138 helix: 0.81 (0.16), residues: 1222 sheet: -2.04 (0.25), residues: 394 loop : -2.36 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.018 0.001 TYR C 109 PHE 0.018 0.001 PHE A 850 TRP 0.010 0.001 TRP D 607 HIS 0.016 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (23858) covalent geometry : angle 0.64023 / 0.32 (32586) SS BOND : bond 0.00365 / 0.25 ( 16) SS BOND : angle 1.44167 / 1.10 ( 32) hydrogen bonds : bond 0.03259 / 2.24 ( 926) hydrogen bonds : angle 4.44192 / 3.16 ( 2658) link_BETA1-4 : bond 0.00991 / 0.49 ( 2) link_BETA1-4 : angle 2.61578 / 1.46 ( 6) link_NAG-ASN : bond 0.00675 / 0.30 ( 12) link_NAG-ASN : angle 3.04968 / 2.53 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 216 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8662 (mpp) cc_final: 0.8307 (ppp) REVERT: A 42 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8183 (p90) REVERT: A 74 MET cc_start: 0.8270 (mmm) cc_final: 0.7743 (mmm) REVERT: A 154 MET cc_start: 0.8581 (mmm) cc_final: 0.8055 (mmm) REVERT: A 436 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8140 (mpp) REVERT: A 530 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: A 549 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: A 575 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7226 (t80) REVERT: A 662 MET cc_start: 0.9394 (tmm) cc_final: 0.9171 (tmm) REVERT: A 789 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.6742 (p-90) REVERT: A 831 CYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6972 (m) REVERT: B 157 MET cc_start: 0.8563 (ptt) cc_final: 0.7966 (ppp) REVERT: B 171 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8453 (mm) REVERT: B 227 ILE cc_start: 0.8036 (mm) cc_final: 0.7777 (mm) REVERT: B 334 MET cc_start: 0.8379 (mmp) cc_final: 0.7776 (pmm) REVERT: B 565 MET cc_start: 0.9057 (mmm) cc_final: 0.8699 (mmm) REVERT: B 654 MET cc_start: 0.7894 (tpp) cc_final: 0.7096 (ttm) REVERT: C 42 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8531 (p90) REVERT: C 74 MET cc_start: 0.8245 (mmm) cc_final: 0.7685 (mmm) REVERT: C 154 MET cc_start: 0.8544 (mmm) cc_final: 0.7934 (mmm) REVERT: C 530 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: C 575 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7467 (t80) REVERT: C 662 MET cc_start: 0.9409 (tmm) cc_final: 0.9103 (tmm) REVERT: C 727 MET cc_start: 0.8353 (ptm) cc_final: 0.7744 (ppp) REVERT: C 831 CYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6903 (m) REVERT: D 142 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7916 (ptp) REVERT: D 171 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8362 (mm) REVERT: D 334 MET cc_start: 0.8513 (mmp) cc_final: 0.8240 (pmm) REVERT: D 339 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8514 (mm) REVERT: D 654 MET cc_start: 0.8079 (tpp) cc_final: 0.7703 (ttm) REVERT: D 746 CYS cc_start: 0.6761 (p) cc_final: 0.6433 (t) outliers start: 93 outliers final: 75 residues processed: 293 average time/residue: 0.1255 time to fit residues: 64.2441 Evaluate side-chains 293 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 203 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 457 CYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 279 optimal weight: 2.9990 chunk 275 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 209 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 237 optimal weight: 30.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 577 GLN C 147 GLN C 177 GLN D 615 ASN D 616 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069749 restraints weight = 91433.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069009 restraints weight = 61818.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069631 restraints weight = 50848.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069958 restraints weight = 43930.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070186 restraints weight = 39885.138| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23888 Z= 0.137 Angle : 0.668 11.714 32660 Z= 0.329 Chirality : 0.045 0.377 3914 Planarity : 0.004 0.043 4132 Dihedral : 5.304 53.056 3341 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.93 % Allowed : 22.58 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.47 (0.16), residues: 3138 helix: 0.91 (0.16), residues: 1206 sheet: -2.08 (0.25), residues: 374 loop : -2.30 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 179 TYR 0.018 0.001 TYR C 109 PHE 0.017 0.001 PHE A 850 TRP 0.011 0.001 TRP D 635 HIS 0.010 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (23858) covalent geometry : angle 0.65907 / 0.33 (32586) SS BOND : bond 0.00356 / 0.24 ( 16) SS BOND : angle 1.21202 / 0.87 ( 32) hydrogen bonds : bond 0.03481 / 2.37 ( 926) hydrogen bonds : angle 4.49368 / 3.19 ( 2658) link_BETA1-4 : bond 0.01382 / 0.70 ( 2) link_BETA1-4 : angle 2.61700 / 1.46 ( 6) link_NAG-ASN : bond 0.00652 / 0.29 ( 12) link_NAG-ASN : angle 3.03531 / 2.52 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.45 seconds wall clock time: 59 minutes 47.09 seconds (3587.09 seconds total)