Starting phenix.real_space_refine on Thu Sep 18 14:51:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjb_43279/09_2025/8vjb_43279_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjb_43279/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vjb_43279/09_2025/8vjb_43279_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjb_43279/09_2025/8vjb_43279_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vjb_43279/09_2025/8vjb_43279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjb_43279/09_2025/8vjb_43279.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.03, per 1000 atoms: 0.21 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: 1.14 Conformation dependent library (CDL) restraints added in 631.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.61 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: 2.55 Time building geometry restraints manager: 1.58 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- 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 : 13.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 870 TYR 0.009 0.001 TYR B 512 PHE 0.030 0.001 PHE A 572 TRP 0.018 0.001 TRP B 559 HIS 0.003 0.000 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00247 (15030) covalent geometry : angle 0.60380 (20352) SS BOND : bond 0.00264 ( 46) SS BOND : angle 0.72365 ( 92) hydrogen bonds : bond 0.25922 ( 324) hydrogen bonds : angle 9.15414 ( 927) *********************** 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 : 0.410 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: 0.1158 time to fit residues: 12.8394 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 : 0.561 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.078670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.050899 restraints weight = 64263.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.053094 restraints weight = 36877.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053346 restraints weight = 23255.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.053635 restraints weight = 19498.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.053600 restraints weight = 18479.836| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 15076 Z= 0.338 Angle : 0.732 11.015 20444 Z= 0.373 Chirality : 0.048 0.155 2214 Planarity : 0.005 0.041 2632 Dihedral : 4.815 43.107 1997 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.20 % Favored : 91.69 % Rotamer: Outliers : 3.27 % Allowed : 24.61 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.20), residues: 1780 helix: -0.33 (0.35), residues: 214 sheet: -0.74 (0.27), residues: 354 loop : -1.47 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 851 TYR 0.023 0.002 TYR A 374 PHE 0.022 0.002 PHE B 506 TRP 0.011 0.002 TRP A 489 HIS 0.005 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00768 (15030) covalent geometry : angle 0.72869 (20352) SS BOND : bond 0.00416 ( 46) SS BOND : angle 1.26652 ( 92) hydrogen bonds : bond 0.05750 ( 324) hydrogen bonds : angle 6.84189 ( 927) *********************** 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 126 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 72 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.7455 (m-90) REVERT: A 442 MET cc_start: 0.9009 (tpp) cc_final: 0.8520 (tpp) REVERT: A 831 MET cc_start: 0.8825 (tpp) cc_final: 0.7788 (mmm) REVERT: B 2 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8022 (pp) REVERT: B 110 MET cc_start: 0.8412 (mmm) cc_final: 0.8158 (mmm) REVERT: B 250 ASP cc_start: 0.8582 (t70) cc_final: 0.8382 (t0) REVERT: B 412 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.7559 (m-90) REVERT: B 442 MET cc_start: 0.9012 (tpp) cc_final: 0.8553 (tpp) outliers start: 54 outliers final: 26 residues processed: 122 average time/residue: 0.1075 time to fit residues: 20.9623 Evaluate side-chains 91 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER 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 412 TRP 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 412 TRP 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 60 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 455 ASN A 589 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN B 788 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.080604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.052387 restraints weight = 64411.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.054180 restraints weight = 32716.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055303 restraints weight = 22301.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.055973 restraints weight = 17952.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056327 restraints weight = 15848.860| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15076 Z= 0.115 Angle : 0.592 9.922 20444 Z= 0.302 Chirality : 0.044 0.152 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.507 41.925 1995 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 3.21 % Allowed : 25.15 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.20), residues: 1780 helix: -0.07 (0.36), residues: 198 sheet: -0.72 (0.28), residues: 344 loop : -1.38 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 40 TYR 0.017 0.001 TYR B 374 PHE 0.019 0.001 PHE A 572 TRP 0.009 0.001 TRP B 897 HIS 0.002 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00258 (15030) covalent geometry : angle 0.59072 (20352) SS BOND : bond 0.00207 ( 46) SS BOND : angle 0.82571 ( 92) hydrogen bonds : bond 0.04891 ( 324) hydrogen bonds : angle 6.33016 ( 927) *********************** 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 115 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 62 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7966 (pp) REVERT: A 38 MET cc_start: 0.8058 (mmt) cc_final: 0.7799 (mmm) REVERT: A 412 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.7480 (m-90) REVERT: A 442 MET cc_start: 0.8855 (tpp) cc_final: 0.8579 (tpp) REVERT: A 797 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8954 (p) REVERT: A 831 MET cc_start: 0.9040 (tpp) cc_final: 0.8167 (mmm) REVERT: B 233 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8978 (pt) REVERT: B 250 ASP cc_start: 0.8470 (t70) cc_final: 0.8243 (t0) REVERT: B 412 TRP cc_start: 0.8827 (OUTLIER) cc_final: 0.7417 (m-90) REVERT: B 442 MET cc_start: 0.8895 (tpp) cc_final: 0.8505 (tpp) REVERT: B 831 MET cc_start: 0.8515 (tpt) cc_final: 0.8297 (tpt) outliers start: 53 outliers final: 26 residues processed: 109 average time/residue: 0.0858 time to fit residues: 15.4759 Evaluate side-chains 92 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU 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 412 TRP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET 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 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET 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 20 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 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 163 optimal weight: 0.0970 chunk 44 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- 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 ** 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** C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.081131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052937 restraints weight = 64202.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.054811 restraints weight = 31474.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.055984 restraints weight = 21172.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.056670 restraints weight = 16859.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.057141 restraints weight = 14843.974| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15076 Z= 0.100 Angle : 0.560 9.453 20444 Z= 0.284 Chirality : 0.043 0.152 2214 Planarity : 0.003 0.042 2632 Dihedral : 4.348 44.950 1995 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.85 % Favored : 92.98 % Rotamer: Outliers : 2.79 % Allowed : 25.03 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.20), residues: 1780 helix: -0.12 (0.36), residues: 202 sheet: -0.53 (0.29), residues: 320 loop : -1.42 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 40 TYR 0.015 0.001 TYR A 374 PHE 0.014 0.001 PHE A 705 TRP 0.009 0.001 TRP B 559 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00223 (15030) covalent geometry : angle 0.55934 (20352) SS BOND : bond 0.00224 ( 46) SS BOND : angle 0.76259 ( 92) hydrogen bonds : bond 0.04057 ( 324) hydrogen bonds : angle 6.06847 ( 927) *********************** 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 114 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 68 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7946 (pp) REVERT: A 38 MET cc_start: 0.7992 (mmt) cc_final: 0.7717 (mmm) REVERT: A 412 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.7393 (m-90) REVERT: A 442 MET cc_start: 0.8792 (tpp) cc_final: 0.8263 (tpp) REVERT: A 635 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: A 831 MET cc_start: 0.9030 (tpp) cc_final: 0.8150 (mmm) REVERT: B 233 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8950 (pt) REVERT: B 250 ASP cc_start: 0.8493 (t70) cc_final: 0.8253 (t0) REVERT: B 412 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.7389 (m-90) REVERT: B 442 MET cc_start: 0.8839 (tpp) cc_final: 0.8500 (tpp) REVERT: B 465 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: B 635 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: B 797 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9054 (p) REVERT: B 831 MET cc_start: 0.8495 (tpt) cc_final: 0.7905 (tpt) outliers start: 46 outliers final: 23 residues processed: 106 average time/residue: 0.0976 time to fit residues: 16.8325 Evaluate side-chains 93 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 790 THR 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 212 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 155 optimal weight: 0.0050 chunk 147 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN B 455 ASN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.079081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.050648 restraints weight = 64260.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.052400 restraints weight = 32773.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053490 restraints weight = 22447.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.054148 restraints weight = 18140.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054479 restraints weight = 16054.938| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15076 Z= 0.217 Angle : 0.621 12.722 20444 Z= 0.311 Chirality : 0.044 0.144 2214 Planarity : 0.004 0.043 2632 Dihedral : 4.506 45.636 1995 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 3.21 % Allowed : 25.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.20), residues: 1780 helix: -0.01 (0.37), residues: 198 sheet: -0.78 (0.28), residues: 344 loop : -1.33 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.019 0.001 TYR A 374 PHE 0.014 0.001 PHE A 506 TRP 0.007 0.002 TRP B 489 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00496 (15030) covalent geometry : angle 0.61814 (20352) SS BOND : bond 0.00315 ( 46) SS BOND : angle 1.07477 ( 92) hydrogen bonds : bond 0.04660 ( 324) hydrogen bonds : angle 6.02542 ( 927) *********************** 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 117 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 64 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 38 MET cc_start: 0.8184 (mmt) cc_final: 0.7954 (mmm) REVERT: A 56 MET cc_start: 0.7822 (ttt) cc_final: 0.7618 (ttt) REVERT: A 412 TRP cc_start: 0.8917 (OUTLIER) cc_final: 0.7488 (m-90) REVERT: A 442 MET cc_start: 0.8910 (tpp) cc_final: 0.8398 (tpp) REVERT: A 635 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: A 797 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9027 (p) REVERT: A 831 MET cc_start: 0.9149 (tpp) cc_final: 0.8309 (mmm) REVERT: B 2 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7946 (pp) REVERT: B 250 ASP cc_start: 0.8536 (t70) cc_final: 0.8323 (t0) REVERT: B 412 TRP cc_start: 0.8898 (OUTLIER) cc_final: 0.7470 (m-90) REVERT: B 442 MET cc_start: 0.8944 (tpp) cc_final: 0.8392 (tpp) REVERT: B 465 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: B 797 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9073 (p) REVERT: B 831 MET cc_start: 0.8362 (tpt) cc_final: 0.8034 (tpt) outliers start: 53 outliers final: 30 residues processed: 111 average time/residue: 0.1091 time to fit residues: 18.9403 Evaluate side-chains 98 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 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 635 GLN 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 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS 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 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 50.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 788 GLN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.079663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.051282 restraints weight = 64352.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.053045 restraints weight = 32525.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054169 restraints weight = 22276.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.054861 restraints weight = 17923.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055265 restraints weight = 15806.285| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15076 Z= 0.146 Angle : 0.575 9.364 20444 Z= 0.291 Chirality : 0.043 0.146 2214 Planarity : 0.003 0.042 2632 Dihedral : 4.441 46.118 1995 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 3.09 % Allowed : 25.70 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.20), residues: 1780 helix: -0.10 (0.36), residues: 202 sheet: -0.76 (0.27), residues: 344 loop : -1.35 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 454 TYR 0.017 0.001 TYR A 374 PHE 0.013 0.001 PHE A 506 TRP 0.007 0.001 TRP B 559 HIS 0.002 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00337 (15030) covalent geometry : angle 0.57267 (20352) SS BOND : bond 0.00211 ( 46) SS BOND : angle 0.94930 ( 92) hydrogen bonds : bond 0.04170 ( 324) hydrogen bonds : angle 5.88191 ( 927) *********************** 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 111 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 60 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 38 MET cc_start: 0.8125 (mmt) cc_final: 0.7906 (mmm) REVERT: A 412 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.7405 (m-90) REVERT: A 442 MET cc_start: 0.8997 (tpp) cc_final: 0.8501 (tpp) REVERT: A 504 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7687 (mtp) REVERT: A 635 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: A 797 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9050 (p) REVERT: A 831 MET cc_start: 0.9165 (tpp) cc_final: 0.8109 (mmm) REVERT: B 2 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7972 (pp) REVERT: B 250 ASP cc_start: 0.8484 (t70) cc_final: 0.8242 (t0) REVERT: B 412 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.7360 (m-90) REVERT: B 442 MET cc_start: 0.9020 (tpp) cc_final: 0.8678 (tpp) REVERT: B 465 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: B 797 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9096 (p) REVERT: B 831 MET cc_start: 0.8254 (tpt) cc_final: 0.7870 (tpt) outliers start: 51 outliers final: 27 residues processed: 103 average time/residue: 0.0914 time to fit residues: 15.7378 Evaluate side-chains 95 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 635 GLN 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 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 112 optimal weight: 0.0980 chunk 125 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.079733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.051329 restraints weight = 63925.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053130 restraints weight = 31921.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054267 restraints weight = 21747.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.054957 restraints weight = 17479.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055382 restraints weight = 15397.443| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2120 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= 0.141 Angle : 0.570 13.743 20444 Z= 0.287 Chirality : 0.043 0.143 2214 Planarity : 0.003 0.042 2632 Dihedral : 4.379 47.355 1995 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 2.79 % Allowed : 25.94 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.20), residues: 1780 helix: -0.14 (0.36), residues: 202 sheet: -0.59 (0.28), residues: 334 loop : -1.41 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.017 0.001 TYR A 374 PHE 0.013 0.001 PHE A 506 TRP 0.010 0.001 TRP B 559 HIS 0.003 0.000 HIS B 865 Details of bonding type rmsd covalent geometry : bond 0.00325 (15030) covalent geometry : angle 0.56821 (20352) SS BOND : bond 0.00233 ( 46) SS BOND : angle 0.89436 ( 92) hydrogen bonds : bond 0.04085 ( 324) hydrogen bonds : angle 5.73979 ( 927) *********************** 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 107 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 61 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8023 (pp) REVERT: A 37 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8918 (mt) REVERT: A 412 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.7362 (m-90) REVERT: A 442 MET cc_start: 0.8978 (tpp) cc_final: 0.8575 (tpp) REVERT: A 635 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: A 831 MET cc_start: 0.9125 (tpp) cc_final: 0.8234 (mmm) REVERT: B 2 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7959 (pp) REVERT: B 250 ASP cc_start: 0.8499 (t70) cc_final: 0.8243 (t0) REVERT: B 412 TRP cc_start: 0.8854 (OUTLIER) cc_final: 0.7368 (m-90) REVERT: B 442 MET cc_start: 0.8999 (tpp) cc_final: 0.8597 (tpp) REVERT: B 465 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: B 504 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7602 (mtp) REVERT: B 831 MET cc_start: 0.8269 (tpt) cc_final: 0.7866 (tpt) outliers start: 46 outliers final: 29 residues processed: 102 average time/residue: 0.1032 time to fit residues: 16.6456 Evaluate side-chains 96 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 412 TRP 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 635 GLN 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 2 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET 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 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 176 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.080599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.052405 restraints weight = 64116.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.054258 restraints weight = 31582.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.055435 restraints weight = 21340.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.056156 restraints weight = 17062.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.056596 restraints weight = 14973.839| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2160 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= 0.098 Angle : 0.564 11.453 20444 Z= 0.285 Chirality : 0.043 0.144 2214 Planarity : 0.003 0.041 2632 Dihedral : 4.293 48.088 1995 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 2.55 % Allowed : 26.36 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.20), residues: 1780 helix: -0.14 (0.36), residues: 202 sheet: -0.47 (0.29), residues: 316 loop : -1.37 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.014 0.001 TYR A 374 PHE 0.019 0.001 PHE C 19 TRP 0.010 0.001 TRP B 559 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00224 (15030) covalent geometry : angle 0.56240 (20352) SS BOND : bond 0.00167 ( 46) SS BOND : angle 0.89914 ( 92) hydrogen bonds : bond 0.03815 ( 324) hydrogen bonds : angle 5.64145 ( 927) *********************** 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 106 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8034 (pp) REVERT: A 37 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8926 (mt) REVERT: A 412 TRP cc_start: 0.8842 (OUTLIER) cc_final: 0.7356 (m-90) REVERT: A 442 MET cc_start: 0.8906 (tpp) cc_final: 0.8458 (tpp) REVERT: A 504 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7645 (mtp) REVERT: A 635 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: A 831 MET cc_start: 0.9098 (tpp) cc_final: 0.8178 (mmm) REVERT: B 250 ASP cc_start: 0.8511 (t70) cc_final: 0.8232 (t0) REVERT: B 412 TRP cc_start: 0.8848 (OUTLIER) cc_final: 0.7382 (m-90) REVERT: B 442 MET cc_start: 0.8938 (tpp) cc_final: 0.8509 (tpp) REVERT: B 465 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: B 831 MET cc_start: 0.8229 (tpt) cc_final: 0.7807 (tpt) outliers start: 42 outliers final: 27 residues processed: 100 average time/residue: 0.0942 time to fit residues: 15.5034 Evaluate side-chains 95 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 207 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET 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 841 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 53 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** 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 = 0.3985 r_free = 0.3985 target = 0.080610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052533 restraints weight = 64280.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.054385 restraints weight = 31597.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.055572 restraints weight = 21237.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.056281 restraints weight = 16928.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.056708 restraints weight = 14854.529| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2237 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= 0.101 Angle : 0.559 11.803 20444 Z= 0.282 Chirality : 0.043 0.173 2214 Planarity : 0.003 0.042 2632 Dihedral : 4.289 48.987 1995 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 2.61 % Allowed : 26.18 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.20), residues: 1780 helix: -0.10 (0.36), residues: 202 sheet: -0.48 (0.28), residues: 330 loop : -1.41 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 479 TYR 0.015 0.001 TYR D 27 PHE 0.013 0.001 PHE A 705 TRP 0.010 0.001 TRP B 559 HIS 0.002 0.000 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00232 (15030) covalent geometry : angle 0.55682 (20352) SS BOND : bond 0.00205 ( 46) SS BOND : angle 0.86409 ( 92) hydrogen bonds : bond 0.03800 ( 324) hydrogen bonds : angle 5.64778 ( 927) *********************** 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 105 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8883 (mt) REVERT: A 98 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8062 (tpp) REVERT: A 412 TRP cc_start: 0.8867 (OUTLIER) cc_final: 0.7401 (m-90) REVERT: A 442 MET cc_start: 0.8916 (tpp) cc_final: 0.8453 (tpp) REVERT: A 504 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: A 635 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 831 MET cc_start: 0.9151 (tpp) cc_final: 0.8277 (mmm) REVERT: B 2 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7931 (pp) REVERT: B 250 ASP cc_start: 0.8517 (t70) cc_final: 0.8237 (t0) REVERT: B 412 TRP cc_start: 0.8848 (OUTLIER) cc_final: 0.7385 (m-90) REVERT: B 442 MET cc_start: 0.8937 (tpp) cc_final: 0.8463 (tpp) REVERT: B 465 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: B 831 MET cc_start: 0.8171 (tpt) cc_final: 0.7759 (tpt) outliers start: 43 outliers final: 28 residues processed: 98 average time/residue: 0.0985 time to fit residues: 16.2447 Evaluate side-chains 97 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 TRP 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 635 GLN 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 2 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 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET 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 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.079555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.051203 restraints weight = 64165.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.053014 restraints weight = 32059.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054150 restraints weight = 21774.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.054818 restraints weight = 17475.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055244 restraints weight = 15411.439| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2365 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= 0.170 Angle : 0.589 11.402 20444 Z= 0.296 Chirality : 0.044 0.139 2214 Planarity : 0.003 0.042 2632 Dihedral : 4.376 49.480 1995 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.13 % Rotamer: Outliers : 2.18 % Allowed : 26.36 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.20), residues: 1780 helix: -0.04 (0.36), residues: 200 sheet: -0.68 (0.27), residues: 354 loop : -1.30 (0.19), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.018 0.001 TYR A 374 PHE 0.013 0.001 PHE A 506 TRP 0.010 0.001 TRP B 559 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00391 (15030) covalent geometry : angle 0.58740 (20352) SS BOND : bond 0.00257 ( 46) SS BOND : angle 0.89833 ( 92) hydrogen bonds : bond 0.04125 ( 324) hydrogen bonds : angle 5.64575 ( 927) ********************** 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 94 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.8893 (OUTLIER) cc_final: 0.7435 (m-90) REVERT: A 442 MET cc_start: 0.8981 (tpp) cc_final: 0.8553 (tpp) REVERT: A 635 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: A 831 MET cc_start: 0.9190 (tpp) cc_final: 0.8320 (mmm) REVERT: B 2 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7973 (pp) REVERT: B 250 ASP cc_start: 0.8527 (t70) cc_final: 0.8280 (t0) REVERT: B 412 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.7378 (m-90) REVERT: B 442 MET cc_start: 0.8993 (tpp) cc_final: 0.8556 (tpp) REVERT: B 465 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: B 831 MET cc_start: 0.8210 (tpt) cc_final: 0.7790 (tpt) outliers start: 36 outliers final: 27 residues processed: 89 average time/residue: 0.0948 time to fit residues: 14.0998 Evaluate side-chains 89 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 412 TRP 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 635 GLN 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 2 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 412 TRP Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 570 VAL 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 20 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** 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 = 0.3972 r_free = 0.3972 target = 0.080079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.051807 restraints weight = 64117.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053646 restraints weight = 31824.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.054802 restraints weight = 21505.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.055525 restraints weight = 17216.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.055940 restraints weight = 15113.433| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15076 Z= 0.119 Angle : 0.569 11.592 20444 Z= 0.286 Chirality : 0.043 0.142 2214 Planarity : 0.003 0.042 2632 Dihedral : 4.311 49.131 1995 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 2.24 % Allowed : 26.30 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.20), residues: 1780 helix: -0.04 (0.36), residues: 200 sheet: -0.44 (0.29), residues: 330 loop : -1.34 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 479 TYR 0.015 0.001 TYR F 27 PHE 0.012 0.001 PHE A 506 TRP 0.011 0.001 TRP B 559 HIS 0.002 0.000 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00276 (15030) covalent geometry : angle 0.56761 (20352) SS BOND : bond 0.00197 ( 46) SS BOND : angle 0.76134 ( 92) hydrogen bonds : bond 0.03902 ( 324) hydrogen bonds : angle 5.53396 ( 927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.21 seconds wall clock time: 56 minutes 5.16 seconds (3365.16 seconds total)