Starting phenix.real_space_refine on Sat Jul 4 17:37:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkp_60202/07_2026/8zkp_60202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkp_60202/07_2026/8zkp_60202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zkp_60202/07_2026/8zkp_60202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkp_60202/07_2026/8zkp_60202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zkp_60202/07_2026/8zkp_60202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkp_60202/07_2026/8zkp_60202.map" } resolution = 2.64 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= 0.083 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 1851 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: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 102 5.16 5 C 13740 2.51 5 N 3378 2.21 5 O 3846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 171 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21087 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5810 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 734} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "H" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "B" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5810 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 734} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "E" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5810 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 734} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "I" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "A" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 298 Unusual residues: {'CDL': 2, 'PEV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 249 Unusual residues: {'CDL': 2, 'PEV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 249 Unusual residues: {'CDL': 2, 'PEV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 4.94, per 1000 atoms: 0.23 Number of scatterers: 21087 At special positions: 0 Unit cell: (121.472, 117.312, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 21 15.00 O 3846 8.00 N 3378 7.00 C 13740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.0 seconds 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4884 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 9 sheets defined 71.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 31 through 49 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.503A pdb=" N ALA A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.736A pdb=" N GLN A 140 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 removed outlier: 4.212A pdb=" N ASN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 223 removed outlier: 4.054A pdb=" N ASP A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 253 removed outlier: 3.657A pdb=" N SER A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 291 removed outlier: 3.771A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 321 removed outlier: 5.578A pdb=" N HIS A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 362 removed outlier: 4.010A pdb=" N GLY A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.954A pdb=" N ARG A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 406 removed outlier: 3.538A pdb=" N ILE A 393 " --> pdb=" O TRP A 389 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.863A pdb=" N LEU A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 458 through 474 removed outlier: 3.755A pdb=" N LEU A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.573A pdb=" N LEU A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.841A pdb=" N PHE A 696 " --> pdb=" O PRO A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.661A pdb=" N GLN A 702 " --> pdb=" O ASN A 698 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY A 704 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 746 removed outlier: 4.174A pdb=" N ILE A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 795 removed outlier: 3.804A pdb=" N THR A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 825 Processing helix chain 'A' and resid 834 through 862 removed outlier: 3.788A pdb=" N ILE A 842 " --> pdb=" O MET A 838 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 893 removed outlier: 4.776A pdb=" N SER A 879 " --> pdb=" O GLY A 875 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 3.643A pdb=" N VAL A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 920 Processing helix chain 'A' and resid 920 through 933 removed outlier: 4.901A pdb=" N THR A 926 " --> pdb=" O ARG A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix Processing helix chain 'A' and resid 935 through 939 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 8 through 29 Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.575A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 56 removed outlier: 3.585A pdb=" N VAL H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 3.595A pdb=" N ALA H 65 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 82 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 31 through 49 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.502A pdb=" N ALA B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.736A pdb=" N GLN B 140 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 176 removed outlier: 4.213A pdb=" N ASN B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 223 removed outlier: 4.053A pdb=" N ASP B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 253 removed outlier: 3.656A pdb=" N SER B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 291 removed outlier: 3.772A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 321 removed outlier: 5.577A pdb=" N HIS B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 335 through 362 removed outlier: 4.010A pdb=" N GLY B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 355 - end of helix Processing helix chain 'B' and resid 373 through 389 removed outlier: 3.955A pdb=" N ARG B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.538A pdb=" N ILE B 393 " --> pdb=" O TRP B 389 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.863A pdb=" N LEU B 421 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 458 through 474 removed outlier: 3.755A pdb=" N LEU B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.573A pdb=" N LEU B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 682 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.841A pdb=" N PHE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 709 removed outlier: 3.662A pdb=" N GLN B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG B 703 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY B 704 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 708 " --> pdb=" O GLY B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 746 removed outlier: 4.173A pdb=" N ILE B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 795 removed outlier: 3.804A pdb=" N THR B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 774 " --> pdb=" O ASP B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 825 Processing helix chain 'B' and resid 834 through 862 removed outlier: 3.789A pdb=" N ILE B 842 " --> pdb=" O MET B 838 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 857 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 893 removed outlier: 4.776A pdb=" N SER B 879 " --> pdb=" O GLY B 875 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 898 removed outlier: 3.643A pdb=" N VAL B 897 " --> pdb=" O SER B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 920 Processing helix chain 'B' and resid 920 through 933 removed outlier: 4.901A pdb=" N THR B 926 " --> pdb=" O ARG B 922 " (cutoff:3.500A) Proline residue: B 927 - end of helix Processing helix chain 'B' and resid 935 through 939 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 8 through 29 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.575A pdb=" N GLU D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.585A pdb=" N VAL D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.596A pdb=" N ALA D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 31 through 49 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 102 through 119 removed outlier: 3.502A pdb=" N ALA E 118 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 119 " --> pdb=" O ARG E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.736A pdb=" N GLN E 140 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 4.212A pdb=" N ASN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 223 removed outlier: 4.054A pdb=" N ASP E 201 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN E 205 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 217 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 253 removed outlier: 3.656A pdb=" N SER E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 291 removed outlier: 3.772A pdb=" N VAL E 268 " --> pdb=" O ASN E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 321 removed outlier: 5.577A pdb=" N HIS E 308 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 335 through 362 removed outlier: 4.010A pdb=" N GLY E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Proline residue: E 355 - end of helix Processing helix chain 'E' and resid 373 through 389 removed outlier: 3.954A pdb=" N ARG E 377 " --> pdb=" O MET E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 406 removed outlier: 3.537A pdb=" N ILE E 393 " --> pdb=" O TRP E 389 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.863A pdb=" N LEU E 421 " --> pdb=" O ARG E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 436 Processing helix chain 'E' and resid 458 through 474 removed outlier: 3.755A pdb=" N LEU E 463 " --> pdb=" O SER E 459 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL E 464 " --> pdb=" O ALA E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 removed outlier: 3.573A pdb=" N LEU E 500 " --> pdb=" O SER E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 682 Processing helix chain 'E' and resid 692 through 696 removed outlier: 3.840A pdb=" N PHE E 696 " --> pdb=" O PRO E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 709 removed outlier: 3.662A pdb=" N GLN E 702 " --> pdb=" O ASN E 698 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG E 703 " --> pdb=" O PRO E 699 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY E 704 " --> pdb=" O ASP E 700 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN E 707 " --> pdb=" O ARG E 703 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 708 " --> pdb=" O GLY E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 746 removed outlier: 4.174A pdb=" N ILE E 735 " --> pdb=" O GLY E 731 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA E 736 " --> pdb=" O ILE E 732 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS E 737 " --> pdb=" O ALA E 733 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 795 removed outlier: 3.804A pdb=" N THR E 773 " --> pdb=" O SER E 769 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 774 " --> pdb=" O ASP E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 825 Processing helix chain 'E' and resid 834 through 862 removed outlier: 3.789A pdb=" N ILE E 842 " --> pdb=" O MET E 838 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 857 " --> pdb=" O LEU E 853 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 893 removed outlier: 4.777A pdb=" N SER E 879 " --> pdb=" O GLY E 875 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL E 880 " --> pdb=" O GLY E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 898 removed outlier: 3.644A pdb=" N VAL E 897 " --> pdb=" O SER E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 920 Processing helix chain 'E' and resid 920 through 933 removed outlier: 4.901A pdb=" N THR E 926 " --> pdb=" O ARG E 922 " (cutoff:3.500A) Proline residue: E 927 - end of helix Processing helix chain 'E' and resid 935 through 939 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 8 through 29 Processing helix chain 'I' and resid 4 through 20 removed outlier: 3.575A pdb=" N GLU I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 56 removed outlier: 3.585A pdb=" N VAL I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 3.596A pdb=" N ALA I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 127 removed outlier: 6.653A pdb=" N LYS A 152 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 126 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN A 150 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 414 removed outlier: 3.623A pdb=" N ASN A 414 " --> pdb=" O LEU A 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 482 removed outlier: 4.833A pdb=" N ARG A 480 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 127 removed outlier: 6.653A pdb=" N LYS B 152 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 126 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN B 150 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 413 through 414 removed outlier: 3.624A pdb=" N ASN B 414 " --> pdb=" O LEU B 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 478 through 482 removed outlier: 4.834A pdb=" N ARG B 480 " --> pdb=" O SER B 721 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 123 through 127 removed outlier: 6.652A pdb=" N LYS E 152 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU E 126 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN E 150 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 413 through 414 removed outlier: 3.624A pdb=" N ASN E 414 " --> pdb=" O LEU E 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 478 through 482 removed outlier: 4.833A pdb=" N ARG E 480 " --> pdb=" O SER E 721 " (cutoff:3.500A) 1377 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 42 1.22 - 1.37: 6782 1.37 - 1.52: 8815 1.52 - 1.67: 5625 1.67 - 1.82: 195 Bond restraints: 21459 Sorted by residual: bond pdb=" C8 PN7 H 101 " pdb=" O8 PN7 H 101 " ideal model delta sigma weight residual 1.223 1.070 0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" C8 PN7 D 101 " pdb=" O8 PN7 D 101 " ideal model delta sigma weight residual 1.223 1.077 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C8 PN7 I 101 " pdb=" O8 PN7 I 101 " ideal model delta sigma weight residual 1.223 1.090 0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" C4 PN7 H 101 " pdb=" O4 PN7 H 101 " ideal model delta sigma weight residual 1.226 1.120 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C4 PN7 D 101 " pdb=" N5 PN7 D 101 " ideal model delta sigma weight residual 1.337 1.440 -0.103 2.00e-02 2.50e+03 2.64e+01 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.12: 28792 6.12 - 12.24: 155 12.24 - 18.36: 30 18.36 - 24.49: 2 24.49 - 30.61: 1 Bond angle restraints: 28980 Sorted by residual: angle pdb=" C7 PN7 H 101 " pdb=" C8 PN7 H 101 " pdb=" N9 PN7 H 101 " ideal model delta sigma weight residual 114.76 145.37 -30.61 3.00e+00 1.11e-01 1.04e+02 angle pdb=" CE1 PN7 I 101 " pdb=" C2 PN7 I 101 " pdb=" C1 PN7 I 101 " ideal model delta sigma weight residual 110.19 90.20 19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" CE1 PN7 H 101 " pdb=" C2 PN7 H 101 " pdb=" C1 PN7 H 101 " ideal model delta sigma weight residual 110.19 91.58 18.61 3.00e+00 1.11e-01 3.85e+01 angle pdb=" N9 PN7 H 101 " pdb=" C8 PN7 H 101 " pdb=" O8 PN7 H 101 " ideal model delta sigma weight residual 122.90 105.00 17.90 3.00e+00 1.11e-01 3.56e+01 angle pdb=" O3P PEV C 201 " pdb=" P PEV C 201 " pdb=" O4P PEV C 201 " ideal model delta sigma weight residual 93.57 110.00 -16.43 3.00e+00 1.11e-01 3.00e+01 ... (remaining 28975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 12227 27.54 - 55.09: 806 55.09 - 82.63: 135 82.63 - 110.17: 3 110.17 - 137.72: 2 Dihedral angle restraints: 13173 sinusoidal: 5577 harmonic: 7596 Sorted by residual: dihedral pdb=" CA TRP E 938 " pdb=" C TRP E 938 " pdb=" N TRP E 939 " pdb=" CA TRP E 939 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TRP A 938 " pdb=" C TRP A 938 " pdb=" N TRP A 939 " pdb=" CA TRP A 939 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TRP B 938 " pdb=" C TRP B 938 " pdb=" N TRP B 939 " pdb=" CA TRP B 939 " ideal model delta harmonic sigma weight residual 180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 13170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2033 0.035 - 0.070: 945 0.070 - 0.104: 299 0.104 - 0.139: 86 0.139 - 0.174: 9 Chirality restraints: 3372 Sorted by residual: chirality pdb=" C2 PEV A1004 " pdb=" C1 PEV A1004 " pdb=" C3 PEV A1004 " pdb=" O2 PEV A1004 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CG LEU E 932 " pdb=" CB LEU E 932 " pdb=" CD1 LEU E 932 " pdb=" CD2 LEU E 932 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CG LEU A 932 " pdb=" CB LEU A 932 " pdb=" CD1 LEU A 932 " pdb=" CD2 LEU A 932 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 3369 not shown) Planarity restraints: 3582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 PN7 H 101 " -0.031 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" C4 PN7 H 101 " 0.015 2.00e-02 2.50e+03 pdb=" C6 PN7 H 101 " -0.043 2.00e-02 2.50e+03 pdb=" N5 PN7 H 101 " 0.055 2.00e-02 2.50e+03 pdb=" O4 PN7 H 101 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PN7 D 101 " -0.028 2.00e-02 2.50e+03 2.36e-02 6.96e+00 pdb=" C7 PN7 D 101 " -0.025 2.00e-02 2.50e+03 pdb=" C8 PN7 D 101 " 0.021 2.00e-02 2.50e+03 pdb=" N9 PN7 D 101 " 0.031 2.00e-02 2.50e+03 pdb=" O8 PN7 D 101 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 821 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C LEU A 821 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU A 821 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 822 " -0.009 2.00e-02 2.50e+03 ... (remaining 3579 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2991 2.75 - 3.29: 20263 3.29 - 3.83: 35425 3.83 - 4.36: 43640 4.36 - 4.90: 76198 Nonbonded interactions: 178517 Sorted by model distance: nonbonded pdb=" N5 PN7 H 101 " pdb=" O8 PN7 H 101 " model vdw 2.213 3.120 nonbonded pdb=" N ASP A 488 " pdb=" OD1 ASP A 488 " model vdw 2.231 3.120 nonbonded pdb=" N ASP E 488 " pdb=" OD1 ASP E 488 " model vdw 2.232 3.120 nonbonded pdb=" N ASP B 488 " pdb=" OD1 ASP B 488 " model vdw 2.233 3.120 nonbonded pdb=" NZ LYS E 381 " pdb=" OD2 ASP I 40 " model vdw 2.273 3.120 ... (remaining 178512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 1003) selection = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 1 through 34) selection = chain 'F' selection = (chain 'G' and resid 1 through 34) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } 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 individual isotropic 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 20.580 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 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 : 0.008 0.460 21462 Z= 0.464 Angle : 1.204 30.606 28980 Z= 0.490 Chirality : 0.044 0.174 3372 Planarity : 0.004 0.035 3582 Dihedral : 17.639 137.717 8289 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.13 % Allowed : 4.11 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.56 (0.15), residues: 2643 helix: -0.78 (0.11), residues: 1782 sheet: -0.47 (0.41), residues: 156 loop : -1.40 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 284 TYR 0.008 0.001 TYR A 300 PHE 0.023 0.002 PHE A 438 TRP 0.012 0.001 TRP E 379 HIS 0.003 0.001 HIS B 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.31 (21459) covalent geometry : angle 1.20355 / 0.49 (28980) hydrogen bonds : bond 0.12926 / 8.81 ( 1377) hydrogen bonds : angle 5.25954 / 3.75 ( 3996) Misc. bond : bond 0.29171 / 10.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 372 time to evaluate : 0.779 Fit side-chains REVERT: A 92 MET cc_start: 0.8288 (mmt) cc_final: 0.7901 (mmt) REVERT: A 197 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 261 PHE cc_start: 0.7989 (t80) cc_final: 0.7763 (t80) REVERT: A 737 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8405 (mttp) REVERT: A 892 MET cc_start: 0.8691 (mmm) cc_final: 0.8485 (mmp) REVERT: F 23 PHE cc_start: 0.7637 (m-80) cc_final: 0.7137 (t80) REVERT: H 32 SER cc_start: 0.8248 (t) cc_final: 0.8023 (t) REVERT: B 197 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 676 MET cc_start: 0.7069 (ttm) cc_final: 0.6833 (ttp) REVERT: B 737 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8310 (mttp) REVERT: B 892 MET cc_start: 0.8699 (mmm) cc_final: 0.8466 (mmp) REVERT: C 23 PHE cc_start: 0.7620 (m-80) cc_final: 0.7146 (t80) REVERT: D 44 MET cc_start: 0.8079 (mmm) cc_final: 0.7877 (mmm) REVERT: E 27 MET cc_start: 0.8162 (mmp) cc_final: 0.7953 (mmp) REVERT: E 174 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 197 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 306 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8586 (m) REVERT: G 23 PHE cc_start: 0.7603 (m-80) cc_final: 0.7175 (t80) outliers start: 45 outliers final: 9 residues processed: 396 average time/residue: 0.6980 time to fit residues: 310.1553 Evaluate side-chains 278 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 268 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 264 ASN A 286 GLN A 414 ASN A 444 ASN A 454 HIS A 466 ASN A 482 GLN A 714 HIS A 722 HIS A 824 GLN A 825 HIS A 832 HIS A 941 GLN H 50 GLN B 60 GLN B 286 GLN B 414 ASN B 454 HIS B 466 ASN B 482 GLN B 714 HIS B 722 HIS B 824 GLN B 825 HIS B 832 HIS B 941 GLN D 50 GLN E 111 GLN E 286 GLN E 414 ASN E 444 ASN E 454 HIS E 466 ASN E 482 GLN E 714 HIS E 722 HIS E 824 GLN E 825 HIS E 832 HIS I 50 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111559 restraints weight = 25597.826| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.78 r_work: 0.3256 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21462 Z= 0.126 Angle : 0.564 10.619 28980 Z= 0.284 Chirality : 0.042 0.171 3372 Planarity : 0.004 0.031 3582 Dihedral : 16.393 142.447 3799 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.51 % Allowed : 10.73 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.04 (0.16), residues: 2643 helix: 0.43 (0.12), residues: 1800 sheet: -0.18 (0.41), residues: 156 loop : -0.71 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 872 TYR 0.008 0.001 TYR B 690 PHE 0.021 0.001 PHE E 438 TRP 0.008 0.001 TRP E 939 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (21459) covalent geometry : angle 0.56410 / 0.28 (28980) hydrogen bonds : bond 0.03908 / 2.67 ( 1377) hydrogen bonds : angle 4.17127 / 3.06 ( 3996) Misc. bond : bond 0.01375 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 0.808 Fit side-chains REVERT: A 76 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8122 (mptm) REVERT: A 176 LEU cc_start: 0.7893 (mp) cc_final: 0.7598 (tt) REVERT: A 197 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 737 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8626 (mttp) REVERT: F 23 PHE cc_start: 0.7912 (m-80) cc_final: 0.6999 (t80) REVERT: H 1 MET cc_start: 0.3279 (OUTLIER) cc_final: 0.2997 (ttt) REVERT: H 32 SER cc_start: 0.8521 (t) cc_final: 0.8272 (t) REVERT: B 176 LEU cc_start: 0.7948 (mp) cc_final: 0.7697 (tt) REVERT: B 197 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 488 ASP cc_start: 0.8444 (m-30) cc_final: 0.8153 (m-30) REVERT: B 676 MET cc_start: 0.6525 (ttm) cc_final: 0.6318 (ttp) REVERT: B 706 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8107 (pt0) REVERT: B 737 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8496 (mttp) REVERT: B 892 MET cc_start: 0.8962 (mmm) cc_final: 0.8736 (mmp) REVERT: C 23 PHE cc_start: 0.7874 (m-80) cc_final: 0.6960 (t80) REVERT: D 1 MET cc_start: 0.3085 (OUTLIER) cc_final: 0.2791 (ttt) REVERT: D 80 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8153 (mp) REVERT: E 174 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7419 (mt-10) REVERT: E 176 LEU cc_start: 0.8037 (mp) cc_final: 0.7743 (tt) REVERT: E 183 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7440 (mmtm) REVERT: E 197 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 306 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8729 (m) REVERT: G 23 PHE cc_start: 0.7933 (m-80) cc_final: 0.7116 (t80) REVERT: I 32 SER cc_start: 0.8404 (t) cc_final: 0.8155 (t) REVERT: I 68 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7391 (ttp80) outliers start: 53 outliers final: 16 residues processed: 323 average time/residue: 0.6617 time to fit residues: 241.7838 Evaluate side-chains 284 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain E residue 874 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 34 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN B 157 GLN B 264 ASN E 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.138333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110421 restraints weight = 25679.221| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.79 r_work: 0.3284 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21462 Z= 0.144 Angle : 0.547 9.441 28980 Z= 0.276 Chirality : 0.042 0.157 3372 Planarity : 0.004 0.032 3582 Dihedral : 15.289 140.625 3790 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.51 % Allowed : 12.43 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.72 (0.16), residues: 2643 helix: 0.93 (0.12), residues: 1794 sheet: 0.08 (0.40), residues: 156 loop : -0.40 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 796 TYR 0.007 0.001 TYR B 690 PHE 0.024 0.001 PHE A 438 TRP 0.009 0.001 TRP B 936 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (21459) covalent geometry : angle 0.54696 / 0.28 (28980) hydrogen bonds : bond 0.03966 / 2.71 ( 1377) hydrogen bonds : angle 4.07560 / 2.99 ( 3996) Misc. bond : bond 0.00078 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 0.811 Fit side-chains REVERT: A 176 LEU cc_start: 0.7852 (mp) cc_final: 0.7536 (tt) REVERT: A 197 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7581 (tm-30) REVERT: F 23 PHE cc_start: 0.7838 (m-80) cc_final: 0.6903 (t80) REVERT: H 1 MET cc_start: 0.3313 (OUTLIER) cc_final: 0.3042 (ttt) REVERT: H 32 SER cc_start: 0.8611 (t) cc_final: 0.8368 (t) REVERT: B 76 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7948 (mptm) REVERT: B 111 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7470 (tp40) REVERT: B 176 LEU cc_start: 0.7929 (mp) cc_final: 0.7660 (tt) REVERT: B 197 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 488 ASP cc_start: 0.8399 (m-30) cc_final: 0.8020 (m-30) REVERT: B 676 MET cc_start: 0.6399 (ttm) cc_final: 0.6154 (ttp) REVERT: B 706 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8037 (pt0) REVERT: B 737 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8411 (mttp) REVERT: B 892 MET cc_start: 0.8959 (mmm) cc_final: 0.8741 (mmp) REVERT: C 23 PHE cc_start: 0.7831 (m-80) cc_final: 0.6865 (t80) REVERT: D 1 MET cc_start: 0.2729 (OUTLIER) cc_final: 0.2354 (ttt) REVERT: D 32 SER cc_start: 0.8577 (t) cc_final: 0.7961 (p) REVERT: E 174 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7472 (mt-10) REVERT: E 176 LEU cc_start: 0.7969 (mp) cc_final: 0.7672 (tt) REVERT: E 197 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7397 (tm-30) REVERT: E 224 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7499 (mtt180) REVERT: G 23 PHE cc_start: 0.7835 (m-80) cc_final: 0.6958 (t80) REVERT: I 32 SER cc_start: 0.8415 (t) cc_final: 0.7527 (p) outliers start: 53 outliers final: 15 residues processed: 303 average time/residue: 0.6573 time to fit residues: 225.2845 Evaluate side-chains 282 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 139 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN B 157 GLN E 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110665 restraints weight = 25783.460| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.80 r_work: 0.3237 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21462 Z= 0.139 Angle : 0.537 9.380 28980 Z= 0.271 Chirality : 0.042 0.164 3372 Planarity : 0.004 0.032 3582 Dihedral : 14.744 138.215 3786 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.93 % Allowed : 12.67 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.10 (0.16), residues: 2643 helix: 1.23 (0.12), residues: 1779 sheet: 0.21 (0.40), residues: 156 loop : -0.26 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 796 TYR 0.007 0.001 TYR B 690 PHE 0.023 0.001 PHE A 438 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (21459) covalent geometry : angle 0.53736 / 0.27 (28980) hydrogen bonds : bond 0.03837 / 2.62 ( 1377) hydrogen bonds : angle 4.01154 / 2.95 ( 3996) Misc. bond : bond 0.00087 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 267 time to evaluate : 0.689 Fit side-chains REVERT: A 176 LEU cc_start: 0.7889 (mp) cc_final: 0.7561 (tt) REVERT: A 197 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 224 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7471 (mtt180) REVERT: F 23 PHE cc_start: 0.7947 (m-80) cc_final: 0.7062 (t80) REVERT: H 1 MET cc_start: 0.3375 (OUTLIER) cc_final: 0.3117 (ttt) REVERT: H 32 SER cc_start: 0.8709 (t) cc_final: 0.8103 (p) REVERT: B 76 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8075 (mptm) REVERT: B 111 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: B 176 LEU cc_start: 0.7879 (mp) cc_final: 0.7601 (tt) REVERT: B 197 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 488 ASP cc_start: 0.8427 (m-30) cc_final: 0.8040 (m-30) REVERT: B 669 MET cc_start: 0.4185 (ttm) cc_final: 0.3929 (ttp) REVERT: B 676 MET cc_start: 0.6491 (ttm) cc_final: 0.6225 (ttp) REVERT: B 706 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8107 (pt0) REVERT: B 737 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8482 (mttp) REVERT: B 892 MET cc_start: 0.8993 (mmm) cc_final: 0.8792 (mmp) REVERT: C 23 PHE cc_start: 0.7924 (m-80) cc_final: 0.7005 (t80) REVERT: D 32 SER cc_start: 0.8670 (t) cc_final: 0.8117 (p) REVERT: E 174 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7578 (mt-10) REVERT: E 176 LEU cc_start: 0.7984 (mp) cc_final: 0.7678 (tt) REVERT: E 197 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7471 (tm-30) REVERT: E 224 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7495 (mtt180) REVERT: G 23 PHE cc_start: 0.7931 (m-80) cc_final: 0.7114 (t80) REVERT: I 32 SER cc_start: 0.8560 (t) cc_final: 0.7779 (p) outliers start: 62 outliers final: 21 residues processed: 304 average time/residue: 0.6189 time to fit residues: 212.4561 Evaluate side-chains 282 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 68 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 157 GLN B 111 GLN E 111 GLN E 157 GLN E 494 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110955 restraints weight = 25583.500| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.78 r_work: 0.3291 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21462 Z= 0.136 Angle : 0.535 8.974 28980 Z= 0.270 Chirality : 0.042 0.191 3372 Planarity : 0.004 0.031 3582 Dihedral : 14.306 135.250 3786 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.65 % Allowed : 13.48 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.32 (0.16), residues: 2643 helix: 1.38 (0.12), residues: 1779 sheet: 0.34 (0.40), residues: 156 loop : -0.12 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 796 TYR 0.007 0.001 TYR E 109 PHE 0.022 0.001 PHE E 438 TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21459) covalent geometry : angle 0.53508 / 0.27 (28980) hydrogen bonds : bond 0.03777 / 2.58 ( 1377) hydrogen bonds : angle 3.98265 / 2.92 ( 3996) Misc. bond : bond 0.00089 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 1.261 Fit side-chains REVERT: A 176 LEU cc_start: 0.7876 (mp) cc_final: 0.7538 (tt) REVERT: A 197 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 224 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7465 (mtt180) REVERT: A 703 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8239 (ttp-170) REVERT: F 23 PHE cc_start: 0.7821 (m-80) cc_final: 0.6894 (t80) REVERT: H 1 MET cc_start: 0.3309 (ttt) cc_final: 0.3058 (ttt) REVERT: H 30 GLU cc_start: 0.8194 (pm20) cc_final: 0.7904 (pm20) REVERT: H 32 SER cc_start: 0.8680 (t) cc_final: 0.8058 (p) REVERT: B 76 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7913 (mptm) REVERT: B 174 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7445 (mp0) REVERT: B 176 LEU cc_start: 0.7943 (mp) cc_final: 0.7657 (tt) REVERT: B 197 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 488 ASP cc_start: 0.8412 (m-30) cc_final: 0.7969 (m-30) REVERT: B 669 MET cc_start: 0.4045 (ttm) cc_final: 0.3821 (ttp) REVERT: B 676 MET cc_start: 0.6289 (ttm) cc_final: 0.6037 (ttp) REVERT: B 706 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7960 (pt0) REVERT: B 737 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8383 (mttp) REVERT: B 892 MET cc_start: 0.8925 (mmm) cc_final: 0.8722 (mmp) REVERT: C 23 PHE cc_start: 0.7799 (m-80) cc_final: 0.6827 (t80) REVERT: D 32 SER cc_start: 0.8662 (t) cc_final: 0.8088 (p) REVERT: D 80 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7986 (mp) REVERT: E 157 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7561 (tp-100) REVERT: E 174 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7494 (mt-10) REVERT: E 176 LEU cc_start: 0.7912 (mp) cc_final: 0.7623 (tt) REVERT: E 197 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7434 (tm-30) REVERT: E 224 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7473 (mtt180) REVERT: G 23 PHE cc_start: 0.7826 (m-80) cc_final: 0.6962 (t80) REVERT: I 32 SER cc_start: 0.8561 (t) cc_final: 0.7716 (p) outliers start: 56 outliers final: 26 residues processed: 297 average time/residue: 0.6499 time to fit residues: 218.1419 Evaluate side-chains 290 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 215 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 254 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 157 GLN B 111 GLN B 157 GLN B 264 ASN E 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109924 restraints weight = 25768.156| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.76 r_work: 0.3256 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21462 Z= 0.110 Angle : 0.514 11.075 28980 Z= 0.258 Chirality : 0.040 0.179 3372 Planarity : 0.004 0.030 3582 Dihedral : 13.756 131.560 3786 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.55 % Allowed : 14.23 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.58 (0.17), residues: 2643 helix: 1.57 (0.12), residues: 1779 sheet: 0.48 (0.41), residues: 156 loop : -0.01 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 796 TYR 0.007 0.001 TYR B 109 PHE 0.020 0.001 PHE E 438 TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (21459) covalent geometry : angle 0.51362 / 0.26 (28980) hydrogen bonds : bond 0.03486 / 2.38 ( 1377) hydrogen bonds : angle 3.89310 / 2.86 ( 3996) Misc. bond : bond 0.00041 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.640 Fit side-chains REVERT: A 157 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7291 (tp-100) REVERT: A 176 LEU cc_start: 0.7855 (mp) cc_final: 0.7541 (tt) REVERT: A 197 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 224 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7386 (mtt180) REVERT: A 703 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8219 (ttp-170) REVERT: F 1 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6461 (tmm) REVERT: F 23 PHE cc_start: 0.7768 (m-80) cc_final: 0.6879 (t80) REVERT: H 1 MET cc_start: 0.3246 (ttt) cc_final: 0.3003 (ttt) REVERT: H 30 GLU cc_start: 0.8122 (pm20) cc_final: 0.7806 (pm20) REVERT: H 32 SER cc_start: 0.8664 (t) cc_final: 0.8097 (p) REVERT: B 76 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7946 (mptm) REVERT: B 176 LEU cc_start: 0.7886 (mp) cc_final: 0.7586 (tt) REVERT: B 197 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 676 MET cc_start: 0.6253 (ttm) cc_final: 0.6009 (ttp) REVERT: B 706 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7954 (pt0) REVERT: B 737 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8422 (mttp) REVERT: B 892 MET cc_start: 0.8947 (mmm) cc_final: 0.8747 (mmp) REVERT: C 23 PHE cc_start: 0.7807 (m-80) cc_final: 0.6875 (t80) REVERT: D 32 SER cc_start: 0.8656 (t) cc_final: 0.8076 (p) REVERT: E 95 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8154 (pt) REVERT: E 174 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7474 (mt-10) REVERT: E 176 LEU cc_start: 0.7843 (mp) cc_final: 0.7539 (tt) REVERT: E 197 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7434 (tm-30) REVERT: E 224 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7445 (mtt180) REVERT: E 773 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8300 (p) REVERT: G 23 PHE cc_start: 0.7845 (m-80) cc_final: 0.6991 (t80) REVERT: I 32 SER cc_start: 0.8610 (t) cc_final: 0.7773 (p) outliers start: 54 outliers final: 28 residues processed: 299 average time/residue: 0.6329 time to fit residues: 213.8176 Evaluate side-chains 287 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 236 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 133 optimal weight: 0.0570 chunk 117 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN B 157 GLN B 494 HIS E 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111423 restraints weight = 25533.082| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.84 r_work: 0.3298 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21462 Z= 0.111 Angle : 0.512 10.281 28980 Z= 0.257 Chirality : 0.041 0.205 3372 Planarity : 0.004 0.030 3582 Dihedral : 13.379 127.793 3786 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.36 % Allowed : 14.99 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.76 (0.17), residues: 2643 helix: 1.65 (0.12), residues: 1791 sheet: 0.60 (0.41), residues: 156 loop : 0.19 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 796 TYR 0.007 0.001 TYR E 109 PHE 0.020 0.001 PHE E 438 TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21459) covalent geometry : angle 0.51212 / 0.26 (28980) hydrogen bonds : bond 0.03450 / 2.36 ( 1377) hydrogen bonds : angle 3.86619 / 2.84 ( 3996) Misc. bond : bond 0.00044 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 0.583 Fit side-chains REVERT: A 176 LEU cc_start: 0.7858 (mp) cc_final: 0.7547 (tt) REVERT: A 197 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 224 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7455 (mtt180) REVERT: A 703 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8222 (ttp-170) REVERT: F 1 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6386 (tmm) REVERT: F 23 PHE cc_start: 0.7729 (m-80) cc_final: 0.6828 (t80) REVERT: H 1 MET cc_start: 0.3253 (OUTLIER) cc_final: 0.3034 (ttt) REVERT: H 30 GLU cc_start: 0.8113 (pm20) cc_final: 0.7791 (pm20) REVERT: H 32 SER cc_start: 0.8627 (t) cc_final: 0.8054 (p) REVERT: H 80 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 76 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7904 (mptm) REVERT: B 176 LEU cc_start: 0.7890 (mp) cc_final: 0.7592 (tt) REVERT: B 197 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 429 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 676 MET cc_start: 0.6162 (ttm) cc_final: 0.5921 (ttp) REVERT: B 706 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7965 (pt0) REVERT: B 737 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8404 (mttp) REVERT: C 23 PHE cc_start: 0.7791 (m-80) cc_final: 0.6841 (t80) REVERT: D 32 SER cc_start: 0.8632 (t) cc_final: 0.8004 (p) REVERT: D 80 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7999 (mp) REVERT: E 176 LEU cc_start: 0.7854 (mp) cc_final: 0.7544 (tt) REVERT: E 197 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7378 (tm-30) REVERT: E 224 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7409 (mtt180) REVERT: E 429 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7619 (mm-30) REVERT: E 773 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8273 (p) REVERT: G 23 PHE cc_start: 0.7829 (m-80) cc_final: 0.6955 (t80) REVERT: I 32 SER cc_start: 0.8551 (t) cc_final: 0.7732 (p) outliers start: 50 outliers final: 30 residues processed: 291 average time/residue: 0.6273 time to fit residues: 206.3089 Evaluate side-chains 291 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 709 LEU Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain E residue 874 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 192 optimal weight: 0.2980 chunk 225 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 157 GLN A 941 GLN B 111 GLN E 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113163 restraints weight = 25424.768| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.84 r_work: 0.3320 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21462 Z= 0.102 Angle : 0.498 9.537 28980 Z= 0.251 Chirality : 0.040 0.195 3372 Planarity : 0.003 0.031 3582 Dihedral : 12.705 119.361 3786 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.27 % Allowed : 15.37 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.98 (0.17), residues: 2643 helix: 1.86 (0.12), residues: 1776 sheet: 0.65 (0.42), residues: 156 loop : 0.21 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 796 TYR 0.007 0.001 TYR B 109 PHE 0.019 0.001 PHE E 438 TRP 0.007 0.001 TRP B 379 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (21459) covalent geometry : angle 0.49779 / 0.25 (28980) hydrogen bonds : bond 0.03237 / 2.21 ( 1377) hydrogen bonds : angle 3.78094 / 2.78 ( 3996) Misc. bond : bond 0.00038 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.656 Fit side-chains REVERT: A 176 LEU cc_start: 0.7797 (mp) cc_final: 0.7520 (tt) REVERT: A 197 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7631 (tm-30) REVERT: F 1 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.6184 (tmm) REVERT: F 23 PHE cc_start: 0.7611 (m-80) cc_final: 0.6690 (t80) REVERT: H 1 MET cc_start: 0.2937 (ttt) cc_final: 0.2568 (ttt) REVERT: H 30 GLU cc_start: 0.8064 (pm20) cc_final: 0.7702 (pm20) REVERT: H 32 SER cc_start: 0.8576 (t) cc_final: 0.7988 (p) REVERT: H 79 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7589 (mttt) REVERT: B 176 LEU cc_start: 0.7888 (mp) cc_final: 0.7590 (tt) REVERT: B 197 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 429 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 440 GLN cc_start: 0.7099 (pt0) cc_final: 0.6842 (pt0) REVERT: B 443 MET cc_start: 0.8806 (mmp) cc_final: 0.8533 (mmt) REVERT: B 676 MET cc_start: 0.6080 (ttm) cc_final: 0.5846 (ttp) REVERT: B 706 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7816 (pt0) REVERT: B 737 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8363 (mttp) REVERT: C 23 PHE cc_start: 0.7744 (m-80) cc_final: 0.6779 (t80) REVERT: D 32 SER cc_start: 0.8612 (t) cc_final: 0.7960 (p) REVERT: D 68 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7775 (ttp80) REVERT: D 80 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8018 (mp) REVERT: E 76 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7867 (mptm) REVERT: E 95 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7994 (pt) REVERT: E 176 LEU cc_start: 0.7865 (mp) cc_final: 0.7570 (tt) REVERT: E 197 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7333 (tm-30) REVERT: E 429 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7549 (mm-30) REVERT: E 773 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8229 (p) REVERT: G 23 PHE cc_start: 0.7735 (m-80) cc_final: 0.6867 (t80) REVERT: I 32 SER cc_start: 0.8470 (t) cc_final: 0.7672 (p) outliers start: 48 outliers final: 29 residues processed: 307 average time/residue: 0.6110 time to fit residues: 212.7960 Evaluate side-chains 293 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain E residue 874 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 162 optimal weight: 0.0170 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 157 GLN B 111 GLN B 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111994 restraints weight = 25515.500| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.83 r_work: 0.3248 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21462 Z= 0.115 Angle : 0.513 9.521 28980 Z= 0.259 Chirality : 0.041 0.193 3372 Planarity : 0.004 0.030 3582 Dihedral : 12.524 115.225 3786 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.17 % Allowed : 15.84 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.04 (0.17), residues: 2643 helix: 1.86 (0.12), residues: 1782 sheet: 0.72 (0.42), residues: 156 loop : 0.31 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 796 TYR 0.006 0.001 TYR E 109 PHE 0.020 0.001 PHE E 438 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (21459) covalent geometry : angle 0.51313 / 0.26 (28980) hydrogen bonds : bond 0.03437 / 2.34 ( 1377) hydrogen bonds : angle 3.83037 / 2.82 ( 3996) Misc. bond : bond 0.00051 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.707 Fit side-chains REVERT: A 111 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7376 (tp-100) REVERT: A 176 LEU cc_start: 0.7823 (mp) cc_final: 0.7608 (tt) REVERT: A 197 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 224 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7444 (mtt180) REVERT: F 1 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6292 (tmm) REVERT: F 23 PHE cc_start: 0.7823 (m-80) cc_final: 0.7019 (t80) REVERT: H 1 MET cc_start: 0.2924 (ttt) cc_final: 0.2556 (ttt) REVERT: H 30 GLU cc_start: 0.8095 (pm20) cc_final: 0.7848 (pm20) REVERT: H 32 SER cc_start: 0.8693 (t) cc_final: 0.8188 (p) REVERT: H 79 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7772 (mttt) REVERT: H 80 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 176 LEU cc_start: 0.7909 (mp) cc_final: 0.7646 (tt) REVERT: B 197 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 429 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 676 MET cc_start: 0.6380 (ttm) cc_final: 0.6113 (ttp) REVERT: B 706 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8007 (pt0) REVERT: B 737 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8509 (mttp) REVERT: C 23 PHE cc_start: 0.7934 (m-80) cc_final: 0.7077 (t80) REVERT: D 32 SER cc_start: 0.8726 (t) cc_final: 0.8173 (p) REVERT: D 68 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7794 (ttp80) REVERT: E 76 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8115 (mptm) REVERT: E 95 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8092 (pt) REVERT: E 111 GLN cc_start: 0.8049 (tp40) cc_final: 0.7666 (tp40) REVERT: E 176 LEU cc_start: 0.7919 (mp) cc_final: 0.7583 (tt) REVERT: E 197 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7407 (tm-30) REVERT: E 429 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7593 (mm-30) REVERT: G 23 PHE cc_start: 0.7935 (m-80) cc_final: 0.7163 (t80) REVERT: I 32 SER cc_start: 0.8626 (t) cc_final: 0.7858 (p) outliers start: 46 outliers final: 34 residues processed: 292 average time/residue: 0.6571 time to fit residues: 217.0238 Evaluate side-chains 298 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain E residue 874 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 494 HIS B 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111031 restraints weight = 25692.559| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.84 r_work: 0.3282 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21462 Z= 0.133 Angle : 0.528 9.581 28980 Z= 0.267 Chirality : 0.042 0.199 3372 Planarity : 0.004 0.029 3582 Dihedral : 12.515 113.427 3786 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 16.22 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.01 (0.17), residues: 2643 helix: 1.82 (0.12), residues: 1785 sheet: 0.74 (0.42), residues: 156 loop : 0.36 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 796 TYR 0.007 0.001 TYR A 300 PHE 0.021 0.001 PHE E 438 TRP 0.010 0.001 TRP B 379 HIS 0.002 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (21459) covalent geometry : angle 0.52824 / 0.27 (28980) hydrogen bonds : bond 0.03592 / 2.45 ( 1377) hydrogen bonds : angle 3.86595 / 2.84 ( 3996) Misc. bond : bond 0.00081 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.673 Fit side-chains REVERT: A 176 LEU cc_start: 0.7826 (mp) cc_final: 0.7566 (tt) REVERT: A 197 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 224 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7455 (mtt180) REVERT: F 1 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6181 (tmm) REVERT: F 23 PHE cc_start: 0.7675 (m-80) cc_final: 0.6767 (t80) REVERT: H 1 MET cc_start: 0.2762 (OUTLIER) cc_final: 0.2388 (ttt) REVERT: H 30 GLU cc_start: 0.8058 (pm20) cc_final: 0.7751 (pm20) REVERT: H 32 SER cc_start: 0.8624 (t) cc_final: 0.8064 (p) REVERT: H 79 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7646 (mttt) REVERT: H 80 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8163 (mp) REVERT: B 111 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7255 (tp-100) REVERT: B 176 LEU cc_start: 0.7934 (mp) cc_final: 0.7677 (tt) REVERT: B 197 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 429 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 706 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7891 (pt0) REVERT: B 737 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8407 (mttp) REVERT: C 23 PHE cc_start: 0.7808 (m-80) cc_final: 0.6858 (t80) REVERT: D 32 SER cc_start: 0.8658 (t) cc_final: 0.8089 (p) REVERT: E 95 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8049 (pt) REVERT: E 111 GLN cc_start: 0.7996 (tp40) cc_final: 0.7669 (tp40) REVERT: E 176 LEU cc_start: 0.7919 (mp) cc_final: 0.7561 (tt) REVERT: E 197 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7339 (tm-30) REVERT: G 23 PHE cc_start: 0.7806 (m-80) cc_final: 0.6946 (t80) REVERT: I 32 SER cc_start: 0.8598 (t) cc_final: 0.7947 (p) REVERT: I 68 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7448 (ttp80) outliers start: 43 outliers final: 32 residues processed: 284 average time/residue: 0.6683 time to fit residues: 214.8839 Evaluate side-chains 294 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 773 THR Chi-restraints excluded: chain E residue 860 GLU Chi-restraints excluded: chain E residue 874 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 216 optimal weight: 0.0980 chunk 207 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN B 111 GLN E 198 GLN E 941 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112120 restraints weight = 25619.270| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.84 r_work: 0.3300 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21462 Z= 0.108 Angle : 0.510 9.248 28980 Z= 0.257 Chirality : 0.041 0.203 3372 Planarity : 0.004 0.030 3582 Dihedral : 12.352 111.522 3786 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.94 % Allowed : 16.31 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.11 (0.17), residues: 2643 helix: 1.91 (0.12), residues: 1782 sheet: 0.71 (0.42), residues: 156 loop : 0.40 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 796 TYR 0.009 0.001 TYR B 109 PHE 0.020 0.001 PHE A 261 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21459) covalent geometry : angle 0.51000 / 0.26 (28980) hydrogen bonds : bond 0.03402 / 2.32 ( 1377) hydrogen bonds : angle 3.82302 / 2.81 ( 3996) Misc. bond : bond 0.00034 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7208.09 seconds wall clock time: 123 minutes 31.98 seconds (7411.98 seconds total)