Starting phenix.real_space_refine on Wed Jan 22 00:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjb_43279/01_2025/8vjb_43279_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjb_43279/01_2025/8vjb_43279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vjb_43279/01_2025/8vjb_43279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjb_43279/01_2025/8vjb_43279.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjb_43279/01_2025/8vjb_43279_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjb_43279/01_2025/8vjb_43279_neut.cif" } resolution = 3.6 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3510 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9312 2.51 5 N 2528 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14688 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6601 Classifications: {'peptide': 816} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 772} Chain breaks: 6 Chain: "B" Number of atoms: 6601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6601 Classifications: {'peptide': 816} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 772} Chain breaks: 6 Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "F" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Time building chain proxies: 8.78, per 1000 atoms: 0.60 Number of scatterers: 14688 At special positions: 0 Unit cell: (135, 119.88, 169.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2728 8.00 N 2528 7.00 C 9312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.02 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 51 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 60 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 2.1 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3428 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 17.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.080A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.178A pdb=" N ASN A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.505A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.761A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.792A pdb=" N PHE A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 643' Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.597A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.074A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.185A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.502A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.768A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.783A pdb=" N PHE B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 692 through 714 Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.869A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 4.069A pdb=" N THR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 4.037A pdb=" N ASP D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 52 through 58 removed outlier: 3.802A pdb=" N LEU D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.811A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 4.081A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 removed outlier: 4.042A pdb=" N ASP F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 52 through 58 removed outlier: 3.756A pdb=" N LEU F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 7.062A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.617A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321 removed outlier: 7.423A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AA9, first strand: chain 'A' and resid 479 through 480 removed outlier: 4.073A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 486 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.573A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.397A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.683A pdb=" N GLU A 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 630 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 627 " --> pdb=" O CYS A 786 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG A 794 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.683A pdb=" N GLU A 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 630 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 627 " --> pdb=" O CYS A 786 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 815 through 822 removed outlier: 5.118A pdb=" N GLN A 833 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS A 872 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 842 through 851 removed outlier: 3.731A pdb=" N GLY A 880 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 905 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.695A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 65 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC2, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.629A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AC4, first strand: chain 'B' and resid 320 through 321 removed outlier: 7.424A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC6, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.012A pdb=" N ARG B 479 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 486 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 530 through 533 removed outlier: 3.576A pdb=" N THR B 530 " --> pdb=" O TYR B 507 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 599 through 605 removed outlier: 5.405A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.687A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 627 " --> pdb=" O CYS B 786 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 794 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.687A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 627 " --> pdb=" O CYS B 786 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 815 through 822 removed outlier: 5.119A pdb=" N GLN B 833 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 842 through 851 removed outlier: 3.732A pdb=" N GLY B 880 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 905 " --> pdb=" O GLY B 880 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 927 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: 5.68 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4826 1.35 - 1.47: 3622 1.47 - 1.59: 6440 1.59 - 1.71: 0 1.71 - 1.83: 142 Bond restraints: 15030 Sorted by residual: bond pdb=" N ASP A 591 " pdb=" CA ASP A 591 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.34e-02 5.57e+03 8.57e+00 bond pdb=" N ASP B 591 " pdb=" CA ASP B 591 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.34e-02 5.57e+03 8.31e+00 bond pdb=" N ALA B 592 " pdb=" CA ALA B 592 " ideal model delta sigma weight residual 1.454 1.486 -0.031 1.16e-02 7.43e+03 7.36e+00 bond pdb=" N ALA A 592 " pdb=" CA ALA A 592 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.16e-02 7.43e+03 7.17e+00 bond pdb=" N THR B 593 " pdb=" CA THR B 593 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.53e-02 4.27e+03 5.03e+00 ... (remaining 15025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 20155 2.45 - 4.90: 168 4.90 - 7.35: 19 7.35 - 9.80: 8 9.80 - 12.25: 2 Bond angle restraints: 20352 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 113.53 108.26 5.27 9.80e-01 1.04e+00 2.89e+01 angle pdb=" N ILE B 692 " pdb=" CA ILE B 692 " pdb=" C ILE B 692 " ideal model delta sigma weight residual 113.53 108.27 5.26 9.80e-01 1.04e+00 2.88e+01 angle pdb=" CB MET A 831 " pdb=" CG MET A 831 " pdb=" SD MET A 831 " ideal model delta sigma weight residual 112.70 124.27 -11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N ASN A 15 " pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " ideal model delta sigma weight residual 114.17 109.85 4.32 1.14e+00 7.69e-01 1.44e+01 angle pdb=" CA LEU C 13 " pdb=" CB LEU C 13 " pdb=" CG LEU C 13 " ideal model delta sigma weight residual 116.30 128.55 -12.25 3.50e+00 8.16e-02 1.22e+01 ... (remaining 20347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 7744 18.02 - 36.04: 1081 36.04 - 54.06: 221 54.06 - 72.09: 49 72.09 - 90.11: 31 Dihedral angle restraints: 9126 sinusoidal: 3818 harmonic: 5308 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -172.54 86.54 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -171.04 85.04 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual -86.00 -163.61 77.61 1 1.00e+01 1.00e-02 7.54e+01 ... (remaining 9123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1380 0.031 - 0.061: 527 0.061 - 0.092: 156 0.092 - 0.122: 130 0.122 - 0.153: 21 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CA THR A 790 " pdb=" N THR A 790 " pdb=" C THR A 790 " pdb=" CB THR A 790 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA THR B 790 " pdb=" N THR B 790 " pdb=" C THR B 790 " pdb=" CB THR B 790 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2211 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 590 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C THR A 590 " -0.032 2.00e-02 2.50e+03 pdb=" O THR A 590 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 591 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 899 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO B 900 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 900 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 900 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 899 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 900 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 900 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 900 " -0.025 5.00e-02 4.00e+02 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 900 2.73 - 3.27: 14950 3.27 - 3.82: 24209 3.82 - 4.36: 27942 4.36 - 4.90: 47401 Nonbonded interactions: 115402 Sorted by model distance: nonbonded pdb=" OG SER A 878 " pdb=" OH TYR A 882 " model vdw 2.190 3.040 nonbonded pdb=" OG SER B 878 " pdb=" OH TYR B 882 " model vdw 2.191 3.040 nonbonded pdb=" O PRO A 716 " pdb=" OH TYR F 27 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.222 3.040 ... (remaining 115397 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.130 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.002 0.039 15030 Z= 0.160 Angle : 0.604 12.248 20352 Z= 0.317 Chirality : 0.043 0.153 2214 Planarity : 0.003 0.045 2632 Dihedral : 17.036 90.106 5560 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 0.24 % Allowed : 28.00 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.46 (0.20), residues: 1780 helix: -0.03 (0.38), residues: 196 sheet: -0.37 (0.28), residues: 358 loop : -1.39 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 559 HIS 0.003 0.000 HIS B 100 PHE 0.030 0.001 PHE A 572 TYR 0.009 0.001 TYR B 512 ARG 0.004 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.8681 (tpp) cc_final: 0.7805 (mmm) REVERT: B 831 MET cc_start: 0.8350 (tpt) cc_final: 0.7303 (mmm) outliers start: 4 outliers final: 3 residues processed: 70 average time/residue: 0.2551 time to fit residues: 28.8715 Evaluate side-chains 69 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 51 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 513 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 513 GLN ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 HIS ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN D 18 GLN F 18 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.078037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050071 restraints weight = 64489.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.052470 restraints weight = 37166.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.052722 restraints weight = 22089.832| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 15030 Z= 0.579 Angle : 0.787 11.024 20352 Z= 0.399 Chirality : 0.049 0.160 2214 Planarity : 0.005 0.042 2632 Dihedral : 4.974 43.011 1997 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.31 % Favored : 91.57 % Rotamer: Outliers : 3.82 % Allowed : 24.12 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.80 (0.20), residues: 1780 helix: -0.43 (0.35), residues: 214 sheet: -0.82 (0.27), residues: 368 loop : -1.54 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 551 HIS 0.007 0.001 HIS A 440 PHE 0.026 0.002 PHE B 506 TYR 0.024 0.002 TYR A 374 ARG 0.005 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 72 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7985 (pp) REVERT: A 38 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: A 412 TRP cc_start: 0.8963 (OUTLIER) cc_final: 0.7508 (m-90) REVERT: A 442 MET cc_start: 0.9078 (tpp) cc_final: 0.8612 (tpp) REVERT: A 482 PHE cc_start: 0.8079 (t80) cc_final: 0.7760 (t80) REVERT: A 831 MET cc_start: 0.8861 (tpp) cc_final: 0.7822 (mmm) REVERT: B 2 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8017 (pp) REVERT: B 110 MET cc_start: 0.8434 (mmm) cc_final: 0.8177 (mmm) REVERT: B 412 TRP cc_start: 0.8958 (OUTLIER) cc_final: 0.7490 (m-90) REVERT: B 442 MET cc_start: 0.9073 (tpp) cc_final: 0.8589 (tpp) REVERT: B 482 PHE cc_start: 0.8100 (t80) cc_final: 0.7730 (t80) REVERT: B 504 MET cc_start: 0.8106 (mmp) cc_final: 0.7748 (mmm) REVERT: B 831 MET cc_start: 0.8401 (tpt) cc_final: 0.8134 (tpt) outliers start: 63 outliers final: 30 residues processed: 130 average time/residue: 0.2298 time to fit residues: 47.7101 Evaluate side-chains 97 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 136 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 78 optimal weight: 50.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.078845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.050267 restraints weight = 64376.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052008 restraints weight = 32767.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.053087 restraints weight = 22518.226| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15030 Z= 0.350 Angle : 0.643 10.363 20352 Z= 0.330 Chirality : 0.045 0.152 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.785 40.684 1995 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.13 % Rotamer: Outliers : 3.70 % Allowed : 25.09 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1780 helix: -0.64 (0.34), residues: 218 sheet: -0.85 (0.28), residues: 344 loop : -1.49 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 414 HIS 0.002 0.001 HIS B 440 PHE 0.018 0.002 PHE A 572 TYR 0.019 0.001 TYR A 374 ARG 0.009 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 60 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8209 (mmt) cc_final: 0.7963 (mmm) REVERT: A 412 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.7434 (m-90) REVERT: A 442 MET cc_start: 0.9055 (tpp) cc_final: 0.8416 (tpp) REVERT: A 465 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: A 797 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8975 (p) REVERT: A 831 MET cc_start: 0.9084 (tpp) cc_final: 0.8216 (mmm) REVERT: B 412 TRP cc_start: 0.8921 (OUTLIER) cc_final: 0.7456 (m-90) REVERT: B 442 MET cc_start: 0.9094 (tpp) cc_final: 0.8405 (tpp) REVERT: B 504 MET cc_start: 0.8147 (mmp) cc_final: 0.7899 (mmm) REVERT: B 797 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.9014 (p) REVERT: B 831 MET cc_start: 0.8572 (tpt) cc_final: 0.8346 (tpt) outliers start: 61 outliers final: 33 residues processed: 116 average time/residue: 0.2195 time to fit residues: 41.6998 Evaluate side-chains 96 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 58 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.050557 restraints weight = 63736.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.052313 restraints weight = 31827.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.053455 restraints weight = 21780.537| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15030 Z= 0.264 Angle : 0.604 9.661 20352 Z= 0.309 Chirality : 0.044 0.150 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.660 43.148 1995 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.13 % Rotamer: Outliers : 3.88 % Allowed : 24.91 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.86 (0.20), residues: 1780 helix: -0.61 (0.34), residues: 218 sheet: -0.86 (0.27), residues: 358 loop : -1.54 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 559 HIS 0.003 0.001 HIS A 429 PHE 0.015 0.001 PHE B 506 TYR 0.018 0.001 TYR A 374 ARG 0.005 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 62 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8113 (pp) REVERT: A 37 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8910 (mt) REVERT: A 38 MET cc_start: 0.8184 (mmt) cc_final: 0.7949 (mmm) REVERT: A 412 TRP cc_start: 0.8940 (OUTLIER) cc_final: 0.7403 (m-90) REVERT: A 442 MET cc_start: 0.9069 (tpp) cc_final: 0.8615 (tpp) REVERT: A 452 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8244 (mm-40) REVERT: A 465 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: A 635 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: A 797 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8993 (p) REVERT: A 831 MET cc_start: 0.9120 (tpp) cc_final: 0.8251 (mmm) REVERT: B 2 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 412 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.7446 (m-90) REVERT: B 442 MET cc_start: 0.9073 (tpp) cc_final: 0.8490 (tpp) REVERT: B 465 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: B 504 MET cc_start: 0.8119 (mmp) cc_final: 0.7840 (mmm) REVERT: B 635 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: B 797 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 831 MET cc_start: 0.8501 (tpt) cc_final: 0.7918 (tpt) outliers start: 64 outliers final: 35 residues processed: 120 average time/residue: 0.2412 time to fit residues: 45.9075 Evaluate side-chains 103 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 56 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 38 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 32 optimal weight: 0.0170 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 overall best weight: 2.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.079944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.050159 restraints weight = 63800.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.051971 restraints weight = 31430.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.053110 restraints weight = 21379.418| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15030 Z= 0.294 Angle : 0.607 9.714 20352 Z= 0.309 Chirality : 0.044 0.149 2214 Planarity : 0.004 0.044 2632 Dihedral : 4.641 43.870 1995 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.20 % Favored : 91.69 % Rotamer: Outliers : 3.94 % Allowed : 25.15 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.83 (0.20), residues: 1780 helix: -0.61 (0.34), residues: 216 sheet: -0.81 (0.27), residues: 354 loop : -1.53 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.002 0.001 HIS A 429 PHE 0.023 0.001 PHE A 572 TYR 0.017 0.001 TYR A 374 ARG 0.008 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 58 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8151 (pp) REVERT: A 38 MET cc_start: 0.8201 (mmt) cc_final: 0.7984 (mmm) REVERT: A 412 TRP cc_start: 0.8965 (OUTLIER) cc_final: 0.7457 (m-90) REVERT: A 442 MET cc_start: 0.9137 (tpp) cc_final: 0.8598 (tpp) REVERT: A 452 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8252 (mm-40) REVERT: A 465 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: A 635 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: A 797 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9050 (p) REVERT: A 831 MET cc_start: 0.9172 (tpp) cc_final: 0.8331 (mmm) REVERT: B 2 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8048 (pp) REVERT: B 412 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.7468 (m-90) REVERT: B 442 MET cc_start: 0.9144 (tpp) cc_final: 0.8767 (tpp) REVERT: B 452 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8325 (mm-40) REVERT: B 465 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8216 (pm20) REVERT: B 504 MET cc_start: 0.8080 (mmp) cc_final: 0.7814 (mmm) REVERT: B 797 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9070 (p) REVERT: B 831 MET cc_start: 0.8471 (tpt) cc_final: 0.8176 (tpt) REVERT: F 27 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7782 (p90) outliers start: 65 outliers final: 41 residues processed: 118 average time/residue: 0.2298 time to fit residues: 43.8249 Evaluate side-chains 110 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 57 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 30.0000 chunk 156 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.079709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.049593 restraints weight = 64836.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.051439 restraints weight = 31657.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052553 restraints weight = 21504.908| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15030 Z= 0.373 Angle : 0.646 9.497 20352 Z= 0.328 Chirality : 0.045 0.149 2214 Planarity : 0.004 0.056 2632 Dihedral : 4.797 45.584 1995 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.82 % Favored : 91.07 % Rotamer: Outliers : 4.12 % Allowed : 25.15 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.85 (0.20), residues: 1780 helix: -0.63 (0.34), residues: 216 sheet: -0.80 (0.27), residues: 350 loop : -1.55 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 559 HIS 0.003 0.001 HIS A 199 PHE 0.020 0.002 PHE E 19 TYR 0.018 0.001 TYR A 374 ARG 0.004 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 57 time to evaluate : 1.730 Fit side-chains REVERT: A 2 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8151 (pp) REVERT: A 38 MET cc_start: 0.8216 (mmt) cc_final: 0.7972 (mmm) REVERT: A 412 TRP cc_start: 0.8982 (OUTLIER) cc_final: 0.7484 (m-90) REVERT: A 442 MET cc_start: 0.9166 (tpp) cc_final: 0.8737 (tpp) REVERT: A 452 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8303 (mm-40) REVERT: A 465 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: A 797 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.9112 (p) REVERT: A 831 MET cc_start: 0.9145 (tpp) cc_final: 0.8062 (mmm) REVERT: B 2 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (pp) REVERT: B 412 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.7591 (m-90) REVERT: B 442 MET cc_start: 0.9178 (tpp) cc_final: 0.8729 (tpp) REVERT: B 452 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8370 (mm-40) REVERT: B 465 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: B 504 MET cc_start: 0.8106 (mmp) cc_final: 0.7852 (mmm) REVERT: B 797 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9141 (p) REVERT: B 831 MET cc_start: 0.8355 (tpt) cc_final: 0.8000 (tpt) REVERT: F 27 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7883 (p90) outliers start: 68 outliers final: 40 residues processed: 120 average time/residue: 0.2151 time to fit residues: 42.5227 Evaluate side-chains 107 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 56 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.081632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.052151 restraints weight = 63824.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.054057 restraints weight = 30661.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.055194 restraints weight = 20606.407| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15030 Z= 0.151 Angle : 0.580 13.793 20352 Z= 0.295 Chirality : 0.044 0.148 2214 Planarity : 0.004 0.044 2632 Dihedral : 4.533 46.349 1995 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.18 % Favored : 93.71 % Rotamer: Outliers : 3.27 % Allowed : 26.30 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.72 (0.20), residues: 1780 helix: -0.56 (0.34), residues: 218 sheet: -0.53 (0.28), residues: 330 loop : -1.50 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 559 HIS 0.003 0.000 HIS A 429 PHE 0.025 0.001 PHE A 572 TYR 0.015 0.001 TYR A 374 ARG 0.005 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 56 time to evaluate : 1.772 Fit side-chains REVERT: A 37 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8927 (mt) REVERT: A 180 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: A 412 TRP cc_start: 0.8867 (OUTLIER) cc_final: 0.7384 (m-90) REVERT: A 442 MET cc_start: 0.9136 (tpp) cc_final: 0.8454 (tpp) REVERT: A 465 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: A 831 MET cc_start: 0.9112 (tpp) cc_final: 0.8266 (mmm) REVERT: B 412 TRP cc_start: 0.8853 (OUTLIER) cc_final: 0.7476 (m-90) REVERT: B 442 MET cc_start: 0.9148 (tpp) cc_final: 0.8852 (tpp) REVERT: B 465 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: B 831 MET cc_start: 0.8286 (tpt) cc_final: 0.7926 (tpt) outliers start: 54 outliers final: 37 residues processed: 103 average time/residue: 0.2051 time to fit residues: 36.1816 Evaluate side-chains 95 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 52 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 157 optimal weight: 0.0980 chunk 147 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 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 = 0.3986 r_free = 0.3986 target = 0.081781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.052391 restraints weight = 63577.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.054337 restraints weight = 30096.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.055518 restraints weight = 20073.351| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15030 Z= 0.148 Angle : 0.561 11.519 20352 Z= 0.286 Chirality : 0.043 0.150 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.374 48.257 1995 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.69 % Favored : 93.20 % Rotamer: Outliers : 2.97 % Allowed : 26.97 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.56 (0.20), residues: 1780 helix: -0.15 (0.36), residues: 200 sheet: -0.47 (0.28), residues: 330 loop : -1.42 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.002 0.000 HIS A 429 PHE 0.016 0.001 PHE A 705 TYR 0.013 0.001 TYR A 374 ARG 0.005 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 61 time to evaluate : 1.926 Fit side-chains REVERT: A 37 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8941 (mt) REVERT: A 412 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.7491 (m-90) REVERT: A 442 MET cc_start: 0.9032 (tpp) cc_final: 0.8746 (tpp) REVERT: A 465 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: A 831 MET cc_start: 0.9162 (tpp) cc_final: 0.8317 (mmm) REVERT: B 180 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: B 412 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.7470 (m-90) REVERT: B 442 MET cc_start: 0.9081 (tpp) cc_final: 0.8799 (tpp) REVERT: B 465 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: B 831 MET cc_start: 0.8266 (tpt) cc_final: 0.7884 (tpt) outliers start: 49 outliers final: 35 residues processed: 105 average time/residue: 0.2150 time to fit residues: 38.4572 Evaluate side-chains 98 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 57 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 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 = 0.3990 r_free = 0.3990 target = 0.081895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.052493 restraints weight = 63570.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.054437 restraints weight = 30291.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055616 restraints weight = 20303.950| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15030 Z= 0.153 Angle : 0.572 15.313 20352 Z= 0.287 Chirality : 0.043 0.165 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.349 48.943 1995 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 2.73 % Allowed : 27.33 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.52 (0.20), residues: 1780 helix: -0.05 (0.36), residues: 200 sheet: -0.45 (0.28), residues: 330 loop : -1.41 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 559 HIS 0.002 0.000 HIS A 429 PHE 0.015 0.001 PHE A 705 TYR 0.013 0.001 TYR D 27 ARG 0.005 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 58 time to evaluate : 1.836 Fit side-chains REVERT: A 37 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8962 (mt) REVERT: A 180 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: A 412 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.7523 (m-90) REVERT: A 442 MET cc_start: 0.9033 (tpp) cc_final: 0.8689 (tpp) REVERT: A 465 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: A 831 MET cc_start: 0.9168 (tpp) cc_final: 0.8325 (mmm) REVERT: B 180 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: B 412 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.7505 (m-90) REVERT: B 442 MET cc_start: 0.9074 (tpp) cc_final: 0.8784 (tpp) REVERT: B 465 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: B 831 MET cc_start: 0.8284 (tpt) cc_final: 0.7904 (tpt) outliers start: 45 outliers final: 35 residues processed: 98 average time/residue: 0.2009 time to fit residues: 34.1172 Evaluate side-chains 100 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 58 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 62 optimal weight: 40.0000 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 40.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 833 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.080122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.050337 restraints weight = 64036.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.052181 restraints weight = 31043.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.053358 restraints weight = 21112.615| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15030 Z= 0.330 Angle : 0.629 12.648 20352 Z= 0.316 Chirality : 0.045 0.146 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.547 49.326 1995 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.97 % Rotamer: Outliers : 3.03 % Allowed : 26.91 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1780 helix: -0.10 (0.36), residues: 200 sheet: -0.58 (0.28), residues: 350 loop : -1.38 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 440 PHE 0.015 0.001 PHE A 482 TYR 0.019 0.001 TYR A 374 ARG 0.007 0.000 ARG B 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 56 time to evaluate : 2.015 Fit side-chains REVERT: A 37 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8984 (mt) REVERT: A 180 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: A 412 TRP cc_start: 0.8961 (OUTLIER) cc_final: 0.7552 (m-90) REVERT: A 442 MET cc_start: 0.9153 (tpp) cc_final: 0.8598 (tpp) REVERT: A 465 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8337 (pm20) REVERT: A 831 MET cc_start: 0.9172 (tpp) cc_final: 0.8330 (mmm) REVERT: B 180 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: B 412 TRP cc_start: 0.8948 (OUTLIER) cc_final: 0.7543 (m-90) REVERT: B 442 MET cc_start: 0.9154 (tpp) cc_final: 0.8581 (tpp) REVERT: B 465 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: B 831 MET cc_start: 0.8344 (tpt) cc_final: 0.7977 (tpt) outliers start: 50 outliers final: 36 residues processed: 100 average time/residue: 0.2034 time to fit residues: 35.8384 Evaluate side-chains 99 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 56 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 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 = 0.3962 r_free = 0.3962 target = 0.080756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.051012 restraints weight = 64079.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.052906 restraints weight = 30901.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.054087 restraints weight = 20882.557| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15030 Z= 0.227 Angle : 0.592 13.358 20352 Z= 0.298 Chirality : 0.044 0.147 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.513 49.605 1995 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.67 % Allowed : 27.21 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.20), residues: 1780 helix: -0.10 (0.36), residues: 200 sheet: -0.44 (0.28), residues: 340 loop : -1.42 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.002 0.001 HIS B 440 PHE 0.013 0.001 PHE B 482 TYR 0.016 0.001 TYR A 374 ARG 0.005 0.000 ARG B 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5288.49 seconds wall clock time: 95 minutes 16.20 seconds (5716.20 seconds total)