Starting phenix.real_space_refine on Sun May 18 22:47:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjb_43279/05_2025/8vjb_43279_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjb_43279/05_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_43279/05_2025/8vjb_43279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjb_43279/05_2025/8vjb_43279.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjb_43279/05_2025/8vjb_43279_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjb_43279/05_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-5687/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: 8.30, per 1000 atoms: 0.57 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: 3.25 Conformation dependent library (CDL) restraints added in 1.5 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: 1.95 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: 4.65 Time building geometry restraints manager: 3.86 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.490 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.440 ------------------------------------------------------------------------------- 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 15076 Z= 0.126 Angle : 0.604 12.248 20444 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 Details of bonding type rmsd hydrogen bonds : bond 0.25922 ( 324) hydrogen bonds : angle 9.15414 ( 927) SS BOND : bond 0.00264 ( 46) SS BOND : angle 0.72365 ( 92) covalent geometry : bond 0.00247 (15030) covalent geometry : angle 0.60380 (20352) *********************** 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 : 1.733 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: 0.2572 time to fit residues: 28.9353 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 : 1.577 ------------------------------------------------------------------------------- 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 15076 Z= 0.395 Angle : 0.791 11.024 20444 Z= 0.401 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 Details of bonding type rmsd hydrogen bonds : bond 0.05799 ( 324) hydrogen bonds : angle 6.88817 ( 927) SS BOND : bond 0.00486 ( 46) SS BOND : angle 1.43144 ( 92) covalent geometry : bond 0.00896 (15030) covalent geometry : angle 0.78704 (20352) *********************** 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 : 1.579 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: 0.2436 time to fit residues: 51.2679 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 : 1.720 ------------------------------------------------------------------------------- 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: 8.9990 chunk 13 optimal weight: 5.9990 chunk 78 optimal weight: 50.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.078561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049947 restraints weight = 64470.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.051663 restraints weight = 32914.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.052744 restraints weight = 22735.956| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 15076 Z= 0.263 Angle : 0.660 10.278 20444 Z= 0.339 Chirality : 0.046 0.153 2214 Planarity : 0.004 0.044 2632 Dihedral : 4.823 40.696 1995 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.87 % Favored : 92.02 % Rotamer: Outliers : 3.82 % Allowed : 25.33 % Favored : 70.85 % 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: -1.84 (0.20), residues: 1780 helix: -0.69 (0.34), residues: 218 sheet: -0.85 (0.28), residues: 344 loop : -1.50 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.007 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 324) hydrogen bonds : angle 6.46564 ( 927) SS BOND : bond 0.00377 ( 46) SS BOND : angle 1.18294 ( 92) covalent geometry : bond 0.00600 (15030) covalent geometry : angle 0.65711 (20352) *********************** 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 123 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 60 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8963 (OUTLIER) cc_final: 0.7442 (m-90) REVERT: A 442 MET cc_start: 0.9098 (tpp) cc_final: 0.8698 (tpp) REVERT: A 465 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: A 797 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9013 (p) REVERT: A 831 MET cc_start: 0.9093 (tpp) cc_final: 0.8222 (mmm) REVERT: B 412 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.7497 (m-90) REVERT: B 442 MET cc_start: 0.9102 (tpp) cc_final: 0.8651 (tpp) REVERT: B 504 MET cc_start: 0.8153 (mmp) cc_final: 0.7901 (mmm) REVERT: B 797 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9029 (p) REVERT: B 831 MET cc_start: 0.8571 (tpt) cc_final: 0.8338 (tpt) REVERT: D 27 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7770 (p90) outliers start: 63 outliers final: 34 residues processed: 118 average time/residue: 0.2211 time to fit residues: 42.3015 Evaluate side-chains 98 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 454 ARG 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 27 TYR 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: 1.9990 chunk 101 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 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 = 0.3933 r_free = 0.3933 target = 0.079473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.049578 restraints weight = 63634.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.051393 restraints weight = 31426.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.052495 restraints weight = 21406.311| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15076 Z= 0.238 Angle : 0.641 9.607 20444 Z= 0.328 Chirality : 0.045 0.152 2214 Planarity : 0.004 0.044 2632 Dihedral : 4.786 43.020 1995 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 4.48 % Allowed : 24.73 % Favored : 70.79 % 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: -1.90 (0.20), residues: 1780 helix: -0.66 (0.34), residues: 216 sheet: -0.89 (0.27), residues: 358 loop : -1.56 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 559 HIS 0.003 0.001 HIS A 429 PHE 0.016 0.002 PHE B 506 TYR 0.019 0.001 TYR A 374 ARG 0.005 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 324) hydrogen bonds : angle 6.18079 ( 927) SS BOND : bond 0.00331 ( 46) SS BOND : angle 1.16764 ( 92) covalent geometry : bond 0.00544 (15030) covalent geometry : angle 0.63742 (20352) *********************** 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 136 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 62 time to evaluate : 1.592 Fit side-chains REVERT: A 2 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8106 (pp) REVERT: A 38 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7899 (mmm) REVERT: A 412 TRP cc_start: 0.8994 (OUTLIER) cc_final: 0.7536 (m-90) REVERT: A 442 MET cc_start: 0.9175 (tpp) cc_final: 0.8640 (tpp) REVERT: A 452 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: A 465 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: A 635 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: A 797 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.9069 (p) REVERT: A 831 MET cc_start: 0.9179 (tpp) cc_final: 0.8363 (mmm) REVERT: B 2 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8020 (pp) REVERT: B 412 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.7477 (m-90) REVERT: B 442 MET cc_start: 0.9184 (tpp) cc_final: 0.8638 (tpp) REVERT: B 452 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8379 (mm-40) REVERT: B 504 MET cc_start: 0.8139 (mmp) cc_final: 0.7832 (mmm) REVERT: B 797 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9085 (p) REVERT: B 831 MET cc_start: 0.8612 (tpt) cc_final: 0.8090 (tpt) REVERT: D 27 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7732 (p90) REVERT: F 27 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7840 (p90) outliers start: 74 outliers final: 39 residues processed: 129 average time/residue: 0.2271 time to fit residues: 46.3712 Evaluate side-chains 109 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 57 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 85 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 454 ARG Chi-restraints excluded: chain A residue 465 GLN 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 377 VAL Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 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 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 27 TYR 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: 6.9990 chunk 88 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 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 E 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.079711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.049585 restraints weight = 64299.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051404 restraints weight = 31528.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052546 restraints weight = 21554.635| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 15076 Z= 0.253 Angle : 0.654 13.568 20444 Z= 0.330 Chirality : 0.045 0.170 2214 Planarity : 0.004 0.045 2632 Dihedral : 4.821 43.829 1995 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 4.67 % Allowed : 24.36 % Favored : 70.97 % 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: -1.92 (0.20), residues: 1780 helix: -0.71 (0.34), residues: 216 sheet: -0.88 (0.27), residues: 364 loop : -1.59 (0.18), residues: 1200 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 0.024 0.002 PHE A 572 TYR 0.018 0.001 TYR A 374 ARG 0.010 0.000 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 324) hydrogen bonds : angle 6.05103 ( 927) SS BOND : bond 0.00354 ( 46) SS BOND : angle 1.21498 ( 92) covalent geometry : bond 0.00580 (15030) covalent geometry : angle 0.64987 (20352) *********************** 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 136 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 59 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (pp) REVERT: A 412 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.7497 (m-90) REVERT: A 442 MET cc_start: 0.9198 (tpp) cc_final: 0.8771 (tpp) REVERT: A 452 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8309 (mm-40) REVERT: A 465 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: A 635 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: A 797 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9095 (p) REVERT: A 831 MET cc_start: 0.9162 (tpp) cc_final: 0.8150 (mmm) REVERT: B 2 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8087 (pp) REVERT: B 412 TRP cc_start: 0.8976 (OUTLIER) cc_final: 0.7517 (m-90) REVERT: B 442 MET cc_start: 0.9213 (tpp) cc_final: 0.8626 (tpp) REVERT: B 452 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8397 (mm-40) REVERT: B 504 MET cc_start: 0.8132 (mmp) cc_final: 0.7827 (mmm) REVERT: B 797 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9119 (p) REVERT: B 831 MET cc_start: 0.8483 (tpt) cc_final: 0.8181 (tpt) REVERT: D 27 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7830 (p90) REVERT: F 27 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7864 (p90) outliers start: 77 outliers final: 46 residues processed: 129 average time/residue: 0.2360 time to fit residues: 48.1787 Evaluate side-chains 116 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 58 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 85 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 378 SER 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 454 ARG 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 841 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 126 CYS 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 378 SER Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 477 TYR 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 27 TYR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 17 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 50.0000 chunk 156 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 80 optimal weight: 50.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.079900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049855 restraints weight = 64730.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.051703 restraints weight = 31416.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.052832 restraints weight = 21325.399| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15076 Z= 0.214 Angle : 0.628 13.005 20444 Z= 0.319 Chirality : 0.045 0.152 2214 Planarity : 0.004 0.044 2632 Dihedral : 4.784 44.986 1995 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.54 % Favored : 91.35 % Rotamer: Outliers : 4.48 % Allowed : 24.73 % Favored : 70.79 % 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: -1.88 (0.20), residues: 1780 helix: -0.72 (0.34), residues: 216 sheet: -0.79 (0.27), residues: 360 loop : -1.57 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.002 0.001 HIS B 429 PHE 0.019 0.001 PHE B 572 TYR 0.017 0.001 TYR A 374 ARG 0.005 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 324) hydrogen bonds : angle 5.90117 ( 927) SS BOND : bond 0.00321 ( 46) SS BOND : angle 1.21089 ( 92) covalent geometry : bond 0.00494 (15030) covalent geometry : angle 0.62442 (20352) *********************** 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 130 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 56 time to evaluate : 1.701 Fit side-chains REVERT: A 2 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (pp) REVERT: A 180 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: A 412 TRP cc_start: 0.8968 (OUTLIER) cc_final: 0.7476 (m-90) REVERT: A 442 MET cc_start: 0.9201 (tpp) cc_final: 0.8665 (tpp) REVERT: A 452 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8277 (mm-40) REVERT: A 465 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: A 797 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.9140 (p) REVERT: A 831 MET cc_start: 0.9149 (tpp) cc_final: 0.8292 (mmm) REVERT: B 2 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8203 (pp) REVERT: B 180 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: B 412 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.7566 (m-90) REVERT: B 442 MET cc_start: 0.9219 (tpp) cc_final: 0.8682 (tpp) REVERT: B 452 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8347 (mm-40) REVERT: B 465 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: B 504 MET cc_start: 0.8113 (mmp) cc_final: 0.7834 (mmm) REVERT: B 797 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9141 (p) REVERT: B 831 MET cc_start: 0.8357 (tpt) cc_final: 0.7994 (tpt) REVERT: D 27 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7797 (p90) REVERT: F 27 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7867 (p90) outliers start: 74 outliers final: 47 residues processed: 125 average time/residue: 0.2330 time to fit residues: 46.3337 Evaluate side-chains 116 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 55 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 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 373 SER 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 454 ARG 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 597 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 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 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 373 SER 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 597 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 27 TYR 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 Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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 148 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** 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 E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.080698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.050838 restraints weight = 64213.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.052737 restraints weight = 30814.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.053893 restraints weight = 20695.438| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15076 Z= 0.138 Angle : 0.588 11.693 20444 Z= 0.299 Chirality : 0.044 0.150 2214 Planarity : 0.004 0.044 2632 Dihedral : 4.660 46.704 1995 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 3.82 % Allowed : 26.00 % Favored : 70.18 % 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: -1.81 (0.20), residues: 1780 helix: -0.62 (0.34), residues: 216 sheet: -0.63 (0.27), residues: 340 loop : -1.56 (0.18), residues: 1224 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 0.021 0.001 PHE B 572 TYR 0.016 0.001 TYR A 374 ARG 0.010 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 324) hydrogen bonds : angle 5.76109 ( 927) SS BOND : bond 0.00248 ( 46) SS BOND : angle 0.98133 ( 92) covalent geometry : bond 0.00319 (15030) covalent geometry : angle 0.58595 (20352) *********************** 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 121 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 58 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8308 (pp) REVERT: A 37 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8950 (mt) REVERT: A 180 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: A 412 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.7430 (m-90) REVERT: A 442 MET cc_start: 0.9206 (tpp) cc_final: 0.8811 (tpp) REVERT: A 465 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: A 831 MET cc_start: 0.9164 (tpp) cc_final: 0.8329 (mmm) REVERT: B 180 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: B 412 TRP cc_start: 0.8906 (OUTLIER) cc_final: 0.7501 (m-90) REVERT: B 442 MET cc_start: 0.9231 (tpp) cc_final: 0.8831 (tpp) REVERT: B 504 MET cc_start: 0.8078 (mmp) cc_final: 0.7791 (mmm) REVERT: B 831 MET cc_start: 0.8331 (tpt) cc_final: 0.7951 (tpt) REVERT: D 27 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.7742 (p90) outliers start: 63 outliers final: 46 residues processed: 115 average time/residue: 0.2043 time to fit residues: 38.7755 Evaluate side-chains 108 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 54 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU 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 377 VAL Chi-restraints excluded: chain A residue 378 SER 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 486 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 597 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 27 SER Chi-restraints excluded: chain B residue 126 CYS 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 412 TRP 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 597 VAL Chi-restraints excluded: chain B residue 604 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 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 14 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.0000 chunk 25 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.080247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.050330 restraints weight = 63929.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.052202 restraints weight = 30840.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.053349 restraints weight = 20830.617| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15076 Z= 0.178 Angle : 0.598 11.095 20444 Z= 0.304 Chirality : 0.044 0.150 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.629 47.176 1995 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 3.88 % Allowed : 25.88 % Favored : 70.24 % 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: -1.79 (0.20), residues: 1780 helix: -0.68 (0.34), residues: 218 sheet: -0.56 (0.28), residues: 340 loop : -1.56 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 559 HIS 0.002 0.001 HIS B 440 PHE 0.023 0.001 PHE B 572 TYR 0.017 0.001 TYR A 374 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 324) hydrogen bonds : angle 5.77968 ( 927) SS BOND : bond 0.00277 ( 46) SS BOND : angle 0.95055 ( 92) covalent geometry : bond 0.00412 (15030) covalent geometry : angle 0.59608 (20352) *********************** 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 119 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 55 time to evaluate : 1.826 Fit side-chains REVERT: A 2 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8317 (pp) REVERT: A 37 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8970 (mt) REVERT: A 180 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: A 412 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.7463 (m-90) REVERT: A 442 MET cc_start: 0.9236 (tpp) cc_final: 0.8815 (tpp) REVERT: A 452 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8167 (mm-40) REVERT: A 465 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: A 831 MET cc_start: 0.9179 (tpp) cc_final: 0.8341 (mmm) REVERT: B 180 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: B 412 TRP cc_start: 0.8934 (OUTLIER) cc_final: 0.7539 (m-90) REVERT: B 442 MET cc_start: 0.9262 (tpp) cc_final: 0.8835 (tpp) REVERT: B 465 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: B 504 MET cc_start: 0.8056 (mmp) cc_final: 0.7769 (mmm) REVERT: B 831 MET cc_start: 0.8360 (tpt) cc_final: 0.7981 (tpt) REVERT: D 27 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7751 (p90) REVERT: F 27 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (p90) outliers start: 64 outliers final: 50 residues processed: 115 average time/residue: 0.2029 time to fit residues: 39.6080 Evaluate side-chains 113 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 52 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain A residue 98 MET 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 373 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 SER 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 477 TYR 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 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 27 SER 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 373 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 411 LEU 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 516 THR 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 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 14 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.080474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.050652 restraints weight = 63818.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052551 restraints weight = 30911.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.053690 restraints weight = 20844.858| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15076 Z= 0.151 Angle : 0.591 10.956 20444 Z= 0.299 Chirality : 0.044 0.149 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.599 47.848 1995 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.58 % Rotamer: Outliers : 4.06 % Allowed : 25.88 % 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: -1.75 (0.20), residues: 1780 helix: -0.63 (0.34), residues: 218 sheet: -0.53 (0.28), residues: 340 loop : -1.53 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.002 0.001 HIS A 429 PHE 0.023 0.001 PHE B 572 TYR 0.016 0.001 TYR A 374 ARG 0.010 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 324) hydrogen bonds : angle 5.68390 ( 927) SS BOND : bond 0.00238 ( 46) SS BOND : angle 1.06233 ( 92) covalent geometry : bond 0.00351 (15030) covalent geometry : angle 0.58835 (20352) *********************** 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 121 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 54 time to evaluate : 1.623 Fit side-chains REVERT: A 37 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8962 (mt) REVERT: A 180 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: A 412 TRP cc_start: 0.8934 (OUTLIER) cc_final: 0.7566 (m-90) REVERT: A 442 MET cc_start: 0.9196 (tpp) cc_final: 0.8777 (tpp) REVERT: A 452 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8123 (mm-40) REVERT: A 465 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: A 831 MET cc_start: 0.9182 (tpp) cc_final: 0.8348 (mmm) REVERT: B 180 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: B 412 TRP cc_start: 0.8906 (OUTLIER) cc_final: 0.7509 (m-90) REVERT: B 442 MET cc_start: 0.9226 (tpp) cc_final: 0.8791 (tpp) REVERT: B 465 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: B 504 MET cc_start: 0.8033 (mmp) cc_final: 0.7756 (mmm) REVERT: B 831 MET cc_start: 0.8330 (tpt) cc_final: 0.7956 (tpt) REVERT: D 27 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7674 (p90) outliers start: 67 outliers final: 52 residues processed: 117 average time/residue: 0.1937 time to fit residues: 38.7748 Evaluate side-chains 115 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 54 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 98 MET 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 373 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 SER 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 477 TYR 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 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 27 SER Chi-restraints excluded: chain B residue 126 CYS 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 378 SER Chi-restraints excluded: chain B residue 411 LEU 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 516 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 604 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 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 14 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 62 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 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 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 = 0.3935 r_free = 0.3935 target = 0.079552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049530 restraints weight = 64255.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051381 restraints weight = 31545.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052521 restraints weight = 21445.391| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15076 Z= 0.239 Angle : 0.644 10.788 20444 Z= 0.325 Chirality : 0.045 0.151 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.756 48.145 1995 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.99 % Favored : 90.96 % Rotamer: Outliers : 3.94 % Allowed : 25.82 % Favored : 70.24 % 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: -1.78 (0.20), residues: 1780 helix: -0.59 (0.35), residues: 214 sheet: -0.66 (0.27), residues: 360 loop : -1.53 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 559 HIS 0.003 0.001 HIS B 199 PHE 0.025 0.002 PHE B 572 TYR 0.017 0.001 TYR A 374 ARG 0.008 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 324) hydrogen bonds : angle 5.78359 ( 927) SS BOND : bond 0.00394 ( 46) SS BOND : angle 1.13252 ( 92) covalent geometry : bond 0.00546 (15030) covalent geometry : angle 0.64074 (20352) ********************** 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 121 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 56 time to evaluate : 1.554 Fit side-chains REVERT: A 37 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8990 (mt) REVERT: A 180 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: A 412 TRP cc_start: 0.8992 (OUTLIER) cc_final: 0.7591 (m-90) REVERT: A 442 MET cc_start: 0.9210 (tpp) cc_final: 0.8538 (tpp) REVERT: A 465 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: B 180 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: B 412 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.7635 (m-90) REVERT: B 442 MET cc_start: 0.9217 (tpp) cc_final: 0.8558 (tpp) REVERT: B 465 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: B 504 MET cc_start: 0.8065 (mmp) cc_final: 0.7790 (mmm) REVERT: B 831 MET cc_start: 0.8411 (tpt) cc_final: 0.8063 (tpt) REVERT: D 27 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7629 (p90) outliers start: 65 outliers final: 54 residues processed: 117 average time/residue: 0.1841 time to fit residues: 37.0506 Evaluate side-chains 118 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 56 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 85 SER 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 373 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 395 ILE 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 486 LEU 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 27 SER 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 373 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 411 LEU 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 486 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 604 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 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 14 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 TYR 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 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: 1.9990 chunk 17 optimal weight: 0.2980 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.081191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.051474 restraints weight = 63938.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053404 restraints weight = 30558.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.054596 restraints weight = 20468.543| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15076 Z= 0.104 Angle : 0.580 11.153 20444 Z= 0.293 Chirality : 0.044 0.149 2214 Planarity : 0.003 0.043 2632 Dihedral : 4.532 49.267 1995 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 3.27 % Allowed : 26.48 % Favored : 70.24 % 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: -1.58 (0.20), residues: 1780 helix: -0.16 (0.36), residues: 200 sheet: -0.45 (0.28), residues: 330 loop : -1.46 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 559 HIS 0.003 0.000 HIS A 429 PHE 0.024 0.001 PHE B 572 TYR 0.013 0.001 TYR A 374 ARG 0.007 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 324) hydrogen bonds : angle 5.55004 ( 927) SS BOND : bond 0.00198 ( 46) SS BOND : angle 0.78813 ( 92) covalent geometry : bond 0.00238 (15030) covalent geometry : angle 0.57880 (20352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5565.35 seconds wall clock time: 97 minutes 53.73 seconds (5873.73 seconds total)