Starting phenix.real_space_refine on Tue Jun 24 05:18:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cls_16718/06_2025/8cls_16718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cls_16718/06_2025/8cls_16718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cls_16718/06_2025/8cls_16718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cls_16718/06_2025/8cls_16718.map" model { file = "/net/cci-nas-00/data/ceres_data/8cls_16718/06_2025/8cls_16718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cls_16718/06_2025/8cls_16718.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 C 8993 2.51 5 N 2447 2.21 5 O 2740 1.98 5 H 13777 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28081 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 12964 Classifications: {'peptide': 837} Link IDs: {'PTRANS': 42, 'TRANS': 794} Chain breaks: 3 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 13182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 13182 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 43, 'TRANS': 809} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 321 Classifications: {'peptide': 24} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 369 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 302 Classifications: {'peptide': 24} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 294 Classifications: {'peptide': 24} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 21} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 324 Classifications: {'peptide': 25} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 325 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 14.29, per 1000 atoms: 0.51 Number of scatterers: 28081 At special positions: 0 Unit cell: (167.181, 145.904, 135.771, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 O 2740 8.00 N 2447 7.00 C 8993 6.00 H 13777 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 527 " distance=2.04 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 539 " distance=2.04 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 545 " distance=2.04 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 618 " distance=2.03 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 643 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 770 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS A 873 " - pdb=" SG CYS B 873 " distance=2.04 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A1258 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 535 " distance=2.10 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 539 " distance=1.93 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 545 " distance=2.73 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 539 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 545 " distance=1.96 Simple disulfide: pdb=" SG CYS B 539 " - pdb=" SG CYS B 545 " distance=2.13 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 564 " distance=2.04 Simple disulfide: pdb=" SG CYS B 564 " - pdb=" SG CYS B 567 " distance=2.05 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 643 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 770 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 981 " - pdb=" SG CYS B1258 " distance=2.04 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS D 6 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS D 18 " distance=2.01 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 14 " distance=2.03 Simple disulfide: pdb=" SG CYS E 10 " - pdb=" SG CYS F 6 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS F 18 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 14 " distance=2.03 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS H 6 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS H 18 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.09 Conformation dependent library (CDL) restraints added in 2.3 seconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3442 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 39 sheets defined 16.5% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.974A pdb=" N ARG A 536 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 639 through 642 removed outlier: 3.902A pdb=" N LYS A 642 " --> pdb=" O PRO A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 642' Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 684 through 694 Processing helix chain 'A' and resid 713 through 717 removed outlier: 4.304A pdb=" N PHE A 716 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 Processing helix chain 'A' and resid 776 through 781 Proline residue: A 779 - end of helix No H-bonds generated for 'chain 'A' and resid 776 through 781' Processing helix chain 'A' and resid 1033 through 1044 Processing helix chain 'A' and resid 1120 through 1124 Processing helix chain 'A' and resid 1173 through 1184 removed outlier: 3.687A pdb=" N THR A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A1182 " --> pdb=" O LEU A1178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A1183 " --> pdb=" O ARG A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1266 removed outlier: 3.669A pdb=" N GLN A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 355 Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.850A pdb=" N ILE B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 4.048A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 594 through 600 removed outlier: 3.994A pdb=" N ILE B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 599 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 683 through 694 removed outlier: 4.074A pdb=" N ASP B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 776 through 781 Proline residue: B 779 - end of helix No H-bonds generated for 'chain 'B' and resid 776 through 781' Processing helix chain 'B' and resid 1024 through 1044 removed outlier: 4.773A pdb=" N VAL B1029 " --> pdb=" O ASP B1025 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B1044 " --> pdb=" O GLN B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1124 Processing helix chain 'B' and resid 1173 through 1179 removed outlier: 3.742A pdb=" N LEU B1178 " --> pdb=" O PRO B1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1268 removed outlier: 4.484A pdb=" N ASN B1265 " --> pdb=" O ALA B1261 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLN B1266 " --> pdb=" O ALA B1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.937A pdb=" N LEU C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 18 removed outlier: 3.539A pdb=" N MET D 13 " --> pdb=" O ALA D 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 15 through 21 Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 21 through 23 No H-bonds generated for 'chain 'G' and resid 21 through 23' Processing helix chain 'H' and resid 7 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.263A pdb=" N ILE A 389 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TYR A 424 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 391 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 421 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLU A 448 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A 423 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 445 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR A 476 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 447 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 522 removed outlier: 4.117A pdb=" N LEU A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 556 removed outlier: 5.120A pdb=" N LEU A 551 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N CYS A 567 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY A 553 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 570 through 572 Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AA7, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA8, first strand: chain 'A' and resid 612 through 614 Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AB1, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.367A pdb=" N CYS A 647 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 673 through 675 removed outlier: 5.862A pdb=" N LEU A 673 " --> pdb=" O MET A 704 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N HIS A 706 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 675 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY A 760 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 736 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 806 through 808 removed outlier: 6.276A pdb=" N ALA A 807 " --> pdb=" O GLU A 916 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 812 through 816 removed outlier: 6.703A pdb=" N MET A 822 " --> pdb=" O GLN A 814 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 821 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 830 through 831 removed outlier: 6.767A pdb=" N GLU A 830 " --> pdb=" O PHE A 844 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AB7, first strand: chain 'A' and resid 933 through 941 removed outlier: 4.219A pdb=" N VAL A 935 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 948 " --> pdb=" O VAL A 935 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA A 937 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 946 " --> pdb=" O ALA A 937 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA A 939 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LYS A 944 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 945 " --> pdb=" O PHE A1153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1127 through 1130 removed outlier: 6.710A pdb=" N GLU A1127 " --> pdb=" O PHE A1140 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE A1140 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP A1129 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU A1138 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 962 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 961 " --> pdb=" O CYS A1169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1208 through 1214 removed outlier: 5.163A pdb=" N ASP A1209 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A1229 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1255 through 1260 Processing sheet with id=AC2, first strand: chain 'A' and resid 1255 through 1260 Processing sheet with id=AC3, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 344 removed outlier: 6.277A pdb=" N LEU B 364 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR B 392 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 366 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE B 389 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TYR B 424 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 391 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR B 419 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ARG B 446 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 421 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLU B 448 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 423 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 445 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 556 removed outlier: 5.196A pdb=" N LEU B 551 " --> pdb=" O CYS B 567 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS B 567 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY B 553 " --> pdb=" O ILE B 565 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AC7, first strand: chain 'B' and resid 584 through 587 removed outlier: 3.638A pdb=" N ARG B 590 " --> pdb=" O PHE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 601 through 604 Processing sheet with id=AC9, first strand: chain 'B' and resid 612 through 614 Processing sheet with id=AD1, first strand: chain 'B' and resid 626 through 628 Processing sheet with id=AD2, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AD3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.144A pdb=" N LEU B 673 " --> pdb=" O MET B 704 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N HIS B 706 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 675 " --> pdb=" O HIS B 706 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE B 762 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR B 737 " --> pdb=" O PHE B 762 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS B 764 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 739 " --> pdb=" O HIS B 764 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 723 Processing sheet with id=AD5, first strand: chain 'B' and resid 811 through 816 removed outlier: 6.315A pdb=" N MET B 822 " --> pdb=" O GLN B 814 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL B 816 " --> pdb=" O SER B 820 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER B 820 " --> pdb=" O VAL B 816 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 830 through 831 removed outlier: 6.928A pdb=" N GLU B 830 " --> pdb=" O PHE B 844 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AD8, first strand: chain 'B' and resid 933 through 939 removed outlier: 4.426A pdb=" N GLU B 934 " --> pdb=" O SER B 950 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B 950 " --> pdb=" O GLU B 934 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1127 through 1130 removed outlier: 6.352A pdb=" N GLU B1127 " --> pdb=" O PHE B1140 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE B1140 " --> pdb=" O GLU B1127 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B1129 " --> pdb=" O GLU B1138 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU B1138 " --> pdb=" O LEU B 968 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS B1169 " --> pdb=" O THR B 960 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR B 962 " --> pdb=" O VAL B1167 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B1167 " --> pdb=" O TYR B 962 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE B 964 " --> pdb=" O PHE B1165 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE B1165 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA B 966 " --> pdb=" O ALA B1163 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B1163 " --> pdb=" O ALA B 966 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1208 through 1214 removed outlier: 5.442A pdb=" N ASP B1209 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B1229 " --> pdb=" O ASP B1209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1255 through 1260 Processing sheet with id=AE3, first strand: chain 'B' and resid 1255 through 1260 377 hydrogen bonds defined for protein. 948 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: 11.48 Time building geometry restraints manager: 8.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 13774 1.04 - 1.25: 2381 1.25 - 1.46: 5322 1.46 - 1.67: 6737 1.67 - 1.88: 163 Bond restraints: 28377 Sorted by residual: bond pdb=" CB CYS B 545 " pdb=" SG CYS B 545 " ideal model delta sigma weight residual 1.808 1.879 -0.071 3.30e-02 9.18e+02 4.66e+00 bond pdb=" CB CYS B 539 " pdb=" SG CYS B 539 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" N SER H 2 " pdb=" CA SER H 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" CB ASN B 766 " pdb=" CG ASN B 766 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.66e+00 bond pdb=" N ASN B 335 " pdb=" CA ASN B 335 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.62e+00 ... (remaining 28372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 50973 2.98 - 5.97: 212 5.97 - 8.95: 6 8.95 - 11.94: 0 11.94 - 14.92: 1 Bond angle restraints: 51192 Sorted by residual: angle pdb=" CA CYS B 539 " pdb=" CB CYS B 539 " pdb=" SG CYS B 539 " ideal model delta sigma weight residual 114.40 99.48 14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" N ARG A 928 " pdb=" CA ARG A 928 " pdb=" C ARG A 928 " ideal model delta sigma weight residual 108.45 114.82 -6.37 1.93e+00 2.68e-01 1.09e+01 angle pdb=" N ARG B 928 " pdb=" CA ARG B 928 " pdb=" C ARG B 928 " ideal model delta sigma weight residual 109.04 113.73 -4.69 1.52e+00 4.33e-01 9.54e+00 angle pdb=" CA PRO B 727 " pdb=" N PRO B 727 " pdb=" CD PRO B 727 " ideal model delta sigma weight residual 112.00 107.79 4.21 1.40e+00 5.10e-01 9.03e+00 angle pdb=" CB LYS B 414 " pdb=" CG LYS B 414 " pdb=" CD LYS B 414 " ideal model delta sigma weight residual 111.30 104.47 6.83 2.30e+00 1.89e-01 8.81e+00 ... (remaining 51187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12200 17.94 - 35.89: 928 35.89 - 53.83: 254 53.83 - 71.77: 197 71.77 - 89.72: 25 Dihedral angle restraints: 13604 sinusoidal: 7362 harmonic: 6242 Sorted by residual: dihedral pdb=" CB CYS B 550 " pdb=" SG CYS B 550 " pdb=" SG CYS B 564 " pdb=" CB CYS B 564 " ideal model delta sinusoidal sigma weight residual -86.00 -172.44 86.44 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS B 531 " pdb=" SG CYS B 531 " pdb=" SG CYS B 545 " pdb=" CB CYS B 545 " ideal model delta sinusoidal sigma weight residual 93.00 172.93 -79.93 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS B 597 " pdb=" SG CYS B 597 " pdb=" SG CYS B 618 " pdb=" CB CYS B 618 " ideal model delta sinusoidal sigma weight residual 93.00 170.23 -77.23 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 13601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1502 0.051 - 0.101: 524 0.101 - 0.152: 142 0.152 - 0.202: 10 0.202 - 0.253: 1 Chirality restraints: 2179 Sorted by residual: chirality pdb=" CA ARG B 393 " pdb=" N ARG B 393 " pdb=" C ARG B 393 " pdb=" CB ARG B 393 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA PHE B 765 " pdb=" N PHE B 765 " pdb=" C PHE B 765 " pdb=" CB PHE B 765 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA LYS A 678 " pdb=" N LYS A 678 " pdb=" C LYS A 678 " pdb=" CB LYS A 678 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 2176 not shown) Planarity restraints: 4313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1200 " -0.178 9.50e-02 1.11e+02 8.77e-02 9.75e+01 pdb=" NE ARG A1200 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A1200 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A1200 " -0.078 2.00e-02 2.50e+03 pdb=" NH2 ARG A1200 " 0.106 2.00e-02 2.50e+03 pdb="HH11 ARG A1200 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A1200 " 0.091 2.00e-02 2.50e+03 pdb="HH21 ARG A1200 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A1200 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 11 " -0.051 9.50e-02 1.11e+02 6.33e-02 8.40e+01 pdb=" NE ARG G 11 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG G 11 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 11 " -0.091 2.00e-02 2.50e+03 pdb=" NH2 ARG G 11 " 0.087 2.00e-02 2.50e+03 pdb="HH11 ARG G 11 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG G 11 " 0.097 2.00e-02 2.50e+03 pdb="HH21 ARG G 11 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG G 11 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 801 " -0.456 9.50e-02 1.11e+02 1.59e-01 7.19e+01 pdb=" NE ARG B 801 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 801 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 801 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B 801 " 0.092 2.00e-02 2.50e+03 pdb="HH11 ARG B 801 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 801 " 0.040 2.00e-02 2.50e+03 pdb="HH21 ARG B 801 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG B 801 " -0.093 2.00e-02 2.50e+03 ... (remaining 4310 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 311 1.95 - 2.61: 33202 2.61 - 3.28: 84640 3.28 - 3.94: 105686 3.94 - 4.60: 167180 Nonbonded interactions: 391019 Sorted by model distance: nonbonded pdb=" H ASN B 335 " pdb="HD21 ASN B 335 " model vdw 1.288 2.100 nonbonded pdb=" O ALA A 840 " pdb=" HG1 THR A 841 " model vdw 1.469 2.450 nonbonded pdb=" O GLU B1023 " pdb=" H ARG B1027 " model vdw 1.479 2.450 nonbonded pdb=" O SER B 701 " pdb=" HG SER B 702 " model vdw 1.489 2.450 nonbonded pdb=" O CYS B 339 " pdb=" H GLU B 361 " model vdw 1.504 2.450 ... (remaining 391014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 335 through 380 or (resid 381 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 382 through 482 or (r \ esid 513 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 514 through 678 or (resid 679 through 680 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 681 through 832 \ or (resid 833 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 834 through 844 or (resid 845 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 846 through 982 or (r \ esid 983 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 984 through 1046 or resid 1118 through 1178 or (resid 1179 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 1180 through 1310)) selection = (chain 'B' and (resid 335 through 479 or (resid 480 through 481 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or (resid 482 and \ (name N or name CA or name C or name O or name CB or name H or name HA or name H \ B2 or name HB3)) or resid 513 through 518 or (resid 519 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 520 through 834 o \ r (resid 835 through 836 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 837 through 969 or (resid 970 through 971 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 972 or (resid 973 through 980 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 981 through 985 or resid 1032 through 1265 \ or (resid 1266 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 1267 through 1310)) } ncs_group { reference = (chain 'C' and (resid 1 through 10 or (resid 11 through 12 and (name N or name C \ A or name C or name O or name H )) or resid 13 through 24)) selection = (chain 'E' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name H )) or resid 13 through 24)) selection = (chain 'G' and (resid 1 through 10 or (resid 11 through 12 and (name N or name C \ A or name C or name O or name H )) or resid 13 through 24)) } ncs_group { reference = (chain 'D' and (resid 2 through 14 or (resid 15 through 16 and (name N or name C \ A or name C or name O or name H )) or resid 17 through 19 or (resid 20 and (name \ N or name CA or name C or name O or name H )) or resid 21 through 24)) selection = (chain 'F' and resid 2 through 24) selection = (chain 'H' and resid 2 through 24) } 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: 4.510 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: 0.460 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 59.780 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.703 14646 Z= 0.408 Angle : 1.003 41.570 19840 Z= 0.542 Chirality : 0.053 0.253 2179 Planarity : 0.011 0.175 2578 Dihedral : 14.264 89.719 5403 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.11 % Favored : 91.61 % Rotamer: Outliers : 1.94 % Allowed : 6.84 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 1812 helix: -3.02 (0.26), residues: 196 sheet: -0.49 (0.26), residues: 367 loop : -1.03 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.005 TRP B1228 HIS 0.013 0.003 HIS A 764 PHE 0.043 0.004 PHE B 404 TYR 0.031 0.006 TYR A1124 ARG 0.038 0.004 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.20160 ( 349) hydrogen bonds : angle 9.72329 ( 948) SS BOND : bond 0.10673 ( 46) SS BOND : angle 8.29664 ( 92) covalent geometry : bond 0.00654 (14600) covalent geometry : angle 0.83105 (19748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 888 MET cc_start: 0.8523 (ttt) cc_final: 0.8312 (ttt) REVERT: B 542 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6091 (mt-10) REVERT: B 858 MET cc_start: 0.8348 (ptm) cc_final: 0.8082 (ptm) REVERT: B 1152 VAL cc_start: 0.8298 (t) cc_final: 0.7756 (m) outliers start: 31 outliers final: 10 residues processed: 182 average time/residue: 0.6383 time to fit residues: 168.9535 Evaluate side-chains 110 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 550 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain E residue 9 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0060 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.082256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063396 restraints weight = 128536.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.066008 restraints weight = 61860.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067708 restraints weight = 37698.768| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 14646 Z= 0.210 Angle : 0.907 31.586 19840 Z= 0.469 Chirality : 0.048 0.351 2179 Planarity : 0.005 0.062 2578 Dihedral : 7.974 57.437 2001 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.91 % Favored : 93.98 % Rotamer: Outliers : 1.38 % Allowed : 9.47 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1812 helix: -2.09 (0.31), residues: 208 sheet: -0.89 (0.26), residues: 363 loop : -0.90 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 522 HIS 0.005 0.001 HIS A 697 PHE 0.017 0.002 PHE G 2 TYR 0.018 0.002 TYR A 388 ARG 0.008 0.001 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 349) hydrogen bonds : angle 7.36703 ( 948) SS BOND : bond 0.03649 ( 46) SS BOND : angle 8.35693 ( 92) covalent geometry : bond 0.00426 (14600) covalent geometry : angle 0.70815 (19748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 MET cc_start: 0.8571 (ttp) cc_final: 0.8335 (ttm) outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 0.6698 time to fit residues: 121.8873 Evaluate side-chains 104 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 151 optimal weight: 0.3980 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063429 restraints weight = 128440.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.066077 restraints weight = 61001.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067800 restraints weight = 37021.037| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 14646 Z= 0.172 Angle : 0.834 31.216 19840 Z= 0.425 Chirality : 0.046 0.257 2179 Planarity : 0.004 0.043 2578 Dihedral : 7.193 52.606 1997 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.17 % Favored : 92.72 % Rotamer: Outliers : 1.32 % Allowed : 9.97 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1812 helix: -1.36 (0.35), residues: 209 sheet: -1.13 (0.25), residues: 372 loop : -0.85 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 522 HIS 0.004 0.001 HIS A 515 PHE 0.028 0.001 PHE B1264 TYR 0.012 0.001 TYR B 737 ARG 0.006 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 349) hydrogen bonds : angle 6.74144 ( 948) SS BOND : bond 0.03548 ( 46) SS BOND : angle 8.16409 ( 92) covalent geometry : bond 0.00324 (14600) covalent geometry : angle 0.62245 (19748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6476 (m-70) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.7495 time to fit residues: 127.6610 Evaluate side-chains 99 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain F residue 13 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1196 GLN B 538 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062813 restraints weight = 130256.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.065455 restraints weight = 61873.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067184 restraints weight = 37533.146| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 14646 Z= 0.196 Angle : 0.862 30.849 19840 Z= 0.435 Chirality : 0.047 0.486 2179 Planarity : 0.004 0.041 2578 Dihedral : 6.753 53.937 1994 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 1.63 % Allowed : 10.98 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1812 helix: -1.22 (0.35), residues: 214 sheet: -1.19 (0.26), residues: 370 loop : -0.91 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 522 HIS 0.006 0.001 HIS A 515 PHE 0.020 0.001 PHE A1165 TYR 0.020 0.001 TYR A1191 ARG 0.005 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 349) hydrogen bonds : angle 6.57056 ( 948) SS BOND : bond 0.03714 ( 46) SS BOND : angle 8.34747 ( 92) covalent geometry : bond 0.00402 (14600) covalent geometry : angle 0.64894 (19748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.7052 (OUTLIER) cc_final: 0.6589 (m-70) REVERT: B 769 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8892 (tt) outliers start: 26 outliers final: 18 residues processed: 111 average time/residue: 0.7829 time to fit residues: 129.8410 Evaluate side-chains 101 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1196 GLN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 0.0050 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.081998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063016 restraints weight = 129396.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065668 restraints weight = 61305.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067406 restraints weight = 37134.897| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 14646 Z= 0.160 Angle : 0.793 30.871 19840 Z= 0.400 Chirality : 0.045 0.300 2179 Planarity : 0.004 0.041 2578 Dihedral : 6.508 55.857 1994 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.07 % Favored : 93.82 % Rotamer: Outliers : 1.25 % Allowed : 11.54 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1812 helix: -1.12 (0.35), residues: 215 sheet: -1.25 (0.26), residues: 365 loop : -0.89 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 522 HIS 0.005 0.001 HIS A 515 PHE 0.014 0.001 PHE A1165 TYR 0.016 0.001 TYR A1191 ARG 0.005 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 349) hydrogen bonds : angle 6.42819 ( 948) SS BOND : bond 0.03654 ( 46) SS BOND : angle 8.01584 ( 92) covalent geometry : bond 0.00281 (14600) covalent geometry : angle 0.57711 (19748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6610 (m-70) REVERT: A 961 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7739 (ppt90) REVERT: A 1161 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8080 (ttt-90) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 0.6012 time to fit residues: 95.0839 Evaluate side-chains 97 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 159 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN ** D 23 ASN ** 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 = 0.3536 r_free = 0.3536 target = 0.080963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061858 restraints weight = 130968.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.064446 restraints weight = 62731.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.066158 restraints weight = 38365.995| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 14646 Z= 0.221 Angle : 0.806 30.696 19840 Z= 0.408 Chirality : 0.046 0.257 2179 Planarity : 0.004 0.040 2578 Dihedral : 6.400 59.713 1991 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.95 % Favored : 92.94 % Rotamer: Outliers : 1.57 % Allowed : 11.36 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.19), residues: 1812 helix: -1.13 (0.34), residues: 216 sheet: -1.26 (0.25), residues: 404 loop : -1.05 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 522 HIS 0.005 0.001 HIS A 515 PHE 0.015 0.001 PHE B1264 TYR 0.017 0.001 TYR A1191 ARG 0.007 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 349) hydrogen bonds : angle 6.43828 ( 948) SS BOND : bond 0.03764 ( 46) SS BOND : angle 7.98072 ( 92) covalent geometry : bond 0.00436 (14600) covalent geometry : angle 0.59702 (19748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6590 (m-70) REVERT: A 961 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7693 (ppt90) REVERT: A 1161 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8136 (ttt-90) REVERT: B 769 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8774 (tt) REVERT: B 1288 ILE cc_start: 0.8966 (pt) cc_final: 0.8630 (mt) outliers start: 25 outliers final: 16 residues processed: 107 average time/residue: 0.6307 time to fit residues: 100.9135 Evaluate side-chains 100 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain G residue 2 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 0.0000 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 171 optimal weight: 0.2980 chunk 137 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN ** D 23 ASN ** 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 = 0.3548 r_free = 0.3548 target = 0.081586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062475 restraints weight = 129934.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065101 restraints weight = 62357.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066848 restraints weight = 37985.399| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 14646 Z= 0.161 Angle : 0.781 30.804 19840 Z= 0.393 Chirality : 0.045 0.265 2179 Planarity : 0.004 0.041 2578 Dihedral : 6.150 58.638 1989 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.18 % Favored : 93.71 % Rotamer: Outliers : 1.51 % Allowed : 11.42 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1812 helix: -0.93 (0.35), residues: 215 sheet: -1.27 (0.25), residues: 403 loop : -0.90 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 522 HIS 0.004 0.001 HIS A 515 PHE 0.015 0.001 PHE B 572 TYR 0.015 0.001 TYR A1191 ARG 0.006 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 349) hydrogen bonds : angle 6.21357 ( 948) SS BOND : bond 0.03729 ( 46) SS BOND : angle 7.96942 ( 92) covalent geometry : bond 0.00283 (14600) covalent geometry : angle 0.56260 (19748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6535 (m-70) REVERT: A 961 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7752 (ppt90) REVERT: A 1161 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8114 (ttt-90) REVERT: B 769 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 1288 ILE cc_start: 0.8944 (pt) cc_final: 0.8632 (mt) outliers start: 24 outliers final: 18 residues processed: 108 average time/residue: 0.6135 time to fit residues: 98.4617 Evaluate side-chains 104 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain B residue 1249 LYS Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain G residue 2 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 102 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.080494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061459 restraints weight = 130811.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.064008 restraints weight = 63301.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065687 restraints weight = 38879.980| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 14646 Z= 0.232 Angle : 0.805 30.753 19840 Z= 0.407 Chirality : 0.046 0.284 2179 Planarity : 0.004 0.042 2578 Dihedral : 6.205 54.999 1989 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.01 % Favored : 92.88 % Rotamer: Outliers : 1.57 % Allowed : 11.29 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1812 helix: -1.02 (0.35), residues: 211 sheet: -1.29 (0.24), residues: 436 loop : -1.03 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 522 HIS 0.004 0.001 HIS A 697 PHE 0.014 0.002 PHE B1264 TYR 0.014 0.001 TYR B 737 ARG 0.008 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 349) hydrogen bonds : angle 6.26341 ( 948) SS BOND : bond 0.03766 ( 46) SS BOND : angle 7.95868 ( 92) covalent geometry : bond 0.00463 (14600) covalent geometry : angle 0.59653 (19748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6594 (m-70) REVERT: A 961 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7750 (ppt90) REVERT: A 1161 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8176 (ttt-90) REVERT: B 769 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 1288 ILE cc_start: 0.9005 (pt) cc_final: 0.8724 (mt) REVERT: H 22 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6669 (t80) outliers start: 25 outliers final: 19 residues processed: 105 average time/residue: 0.5693 time to fit residues: 90.1777 Evaluate side-chains 103 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain B residue 1249 LYS Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain H residue 22 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 147 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062345 restraints weight = 130112.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064987 restraints weight = 62537.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066711 restraints weight = 38063.939| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 14646 Z= 0.157 Angle : 0.778 30.860 19840 Z= 0.390 Chirality : 0.045 0.282 2179 Planarity : 0.004 0.043 2578 Dihedral : 5.993 54.240 1989 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 1.38 % Allowed : 11.67 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1812 helix: -0.87 (0.36), residues: 210 sheet: -1.29 (0.25), residues: 413 loop : -0.87 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 522 HIS 0.003 0.001 HIS B 706 PHE 0.014 0.001 PHE B1264 TYR 0.009 0.001 TYR B 962 ARG 0.006 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 349) hydrogen bonds : angle 6.02027 ( 948) SS BOND : bond 0.03721 ( 46) SS BOND : angle 7.95832 ( 92) covalent geometry : bond 0.00269 (14600) covalent geometry : angle 0.55919 (19748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6526 (m-70) REVERT: A 961 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7726 (ppt90) REVERT: A 1161 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8151 (ttt-90) REVERT: B 769 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 1288 ILE cc_start: 0.9006 (pt) cc_final: 0.8731 (mt) REVERT: H 22 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6637 (t80) outliers start: 22 outliers final: 18 residues processed: 106 average time/residue: 0.5894 time to fit residues: 94.8759 Evaluate side-chains 102 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 873 CYS Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain B residue 1249 LYS Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain H residue 22 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 179 optimal weight: 0.0970 chunk 125 optimal weight: 0.5980 chunk 151 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN ** D 23 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.081913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062805 restraints weight = 129308.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065439 restraints weight = 62091.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.067181 restraints weight = 37940.698| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 14646 Z= 0.144 Angle : 0.769 30.814 19840 Z= 0.384 Chirality : 0.045 0.297 2179 Planarity : 0.004 0.044 2578 Dihedral : 5.797 54.636 1989 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 1.51 % Allowed : 11.86 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1812 helix: -0.83 (0.36), residues: 212 sheet: -1.20 (0.25), residues: 413 loop : -0.77 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 522 HIS 0.003 0.001 HIS A 706 PHE 0.013 0.001 PHE B1264 TYR 0.008 0.001 TYR B 902 ARG 0.005 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 349) hydrogen bonds : angle 5.87201 ( 948) SS BOND : bond 0.03705 ( 46) SS BOND : angle 7.96389 ( 92) covalent geometry : bond 0.00232 (14600) covalent geometry : angle 0.54650 (19748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 480 is missing expected H atoms. Skipping. Residue LYS 482 is missing expected H atoms. Skipping. Residue LYS 836 is missing expected H atoms. Skipping. Residue THR 973 is missing expected H atoms. Skipping. Residue TYR 980 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue THR 982 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue ALA 9 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6418 (m-70) REVERT: A 961 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7702 (ppt90) REVERT: A 1161 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8152 (ttt-90) REVERT: B 1288 ILE cc_start: 0.9002 (pt) cc_final: 0.8719 (mt) REVERT: H 22 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6654 (t80) outliers start: 24 outliers final: 18 residues processed: 109 average time/residue: 0.6099 time to fit residues: 99.0546 Evaluate side-chains 104 residues out of total 1657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 873 CYS Chi-restraints excluded: chain B residue 980 TYR Chi-restraints excluded: chain B residue 1249 LYS Chi-restraints excluded: chain D residue 18 CYS Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain H residue 22 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 0.6980 chunk 111 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.081941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062975 restraints weight = 128943.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065593 restraints weight = 61319.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.067307 restraints weight = 37346.839| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 14646 Z= 0.143 Angle : 0.762 30.747 19840 Z= 0.380 Chirality : 0.045 0.295 2179 Planarity : 0.004 0.039 2578 Dihedral : 5.652 54.960 1989 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 1.32 % Allowed : 12.11 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1812 helix: -0.75 (0.36), residues: 212 sheet: -1.14 (0.25), residues: 426 loop : -0.70 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 522 HIS 0.003 0.001 HIS A 697 PHE 0.013 0.001 PHE B1136 TYR 0.008 0.001 TYR B 902 ARG 0.005 0.000 ARG A1179 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 349) hydrogen bonds : angle 5.76848 ( 948) SS BOND : bond 0.03699 ( 46) SS BOND : angle 7.95233 ( 92) covalent geometry : bond 0.00228 (14600) covalent geometry : angle 0.53761 (19748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8448.91 seconds wall clock time: 149 minutes 29.03 seconds (8969.03 seconds total)