Starting phenix.real_space_refine on Mon May 4 15:44:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkp_60202/05_2026/8zkp_60202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkp_60202/05_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_60202/05_2026/8zkp_60202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkp_60202/05_2026/8zkp_60202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zkp_60202/05_2026/8zkp_60202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkp_60202/05_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 5.11, per 1000 atoms: 0.24 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: 1.94 Conformation dependent library (CDL) restraints added in 1.2 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: 0.83 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: 4.03 Time building geometry restraints manager: 2.53 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=" CB7 CDL B1002 " pdb=" OB8 CDL B1002 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.75e+01 bond pdb=" CB7 CDL E1001 " pdb=" OB8 CDL E1001 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.69e+01 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.12: 28861 6.12 - 12.24: 101 12.24 - 18.36: 15 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=" C51 CDL A1002 " pdb=" CB5 CDL A1002 " pdb=" OB6 CDL A1002 " ideal model delta sigma weight residual 111.33 121.73 -10.40 1.32e+00 5.72e-01 6.19e+01 angle pdb=" C11 CDL A1002 " pdb=" CA5 CDL A1002 " pdb=" OA6 CDL A1002 " ideal model delta sigma weight residual 111.33 121.14 -9.81 1.32e+00 5.72e-01 5.51e+01 angle pdb=" C11 CDL B1002 " pdb=" CA5 CDL B1002 " pdb=" OA6 CDL B1002 " ideal model delta sigma weight residual 111.33 120.63 -9.30 1.32e+00 5.72e-01 4.95e+01 angle pdb=" C51 CDL A1001 " pdb=" CB5 CDL A1001 " pdb=" OB6 CDL A1001 " ideal model delta sigma weight residual 111.33 120.47 -9.14 1.32e+00 5.72e-01 4.78e+01 ... (remaining 28975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 12160 27.54 - 55.09: 785 55.09 - 82.63: 124 82.63 - 110.17: 6 110.17 - 137.72: 2 Dihedral angle restraints: 13077 sinusoidal: 5481 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 13074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2032 0.035 - 0.070: 945 0.070 - 0.104: 302 0.104 - 0.139: 84 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.030 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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= 0.530 Angle : 1.135 30.606 28980 Z= 0.527 Chirality : 0.044 0.174 3372 Planarity : 0.004 0.035 3582 Dihedral : 17.505 137.717 8193 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 covalent geometry : bond 0.00755 (21459) covalent geometry : angle 1.13490 (28980) hydrogen bonds : bond 0.12926 ( 1377) hydrogen bonds : angle 5.25954 ( 3996) Misc. bond : bond 0.29171 ( 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 : 0.785 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: 0.7324 time to fit residues: 323.6105 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 : 0.690 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 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: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111358 restraints weight = 25612.147| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.78 r_work: 0.3306 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21462 Z= 0.126 Angle : 0.560 10.445 28980 Z= 0.284 Chirality : 0.041 0.147 3372 Planarity : 0.004 0.032 3582 Dihedral : 16.113 142.569 3703 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.32 % Allowed : 10.83 % Favored : 86.86 % 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: 0.45 (0.12), residues: 1782 sheet: -0.18 (0.41), residues: 156 loop : -0.74 (0.23), residues: 705 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 covalent geometry : bond 0.00281 (21459) covalent geometry : angle 0.55965 (28980) hydrogen bonds : bond 0.04007 ( 1377) hydrogen bonds : angle 4.18751 ( 3996) Misc. bond : bond 0.00180 ( 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 340 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.799 Fit side-chains REVERT: A 176 LEU cc_start: 0.7867 (mp) cc_final: 0.7565 (tt) REVERT: A 197 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 737 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8551 (mttp) REVERT: A 892 MET cc_start: 0.8873 (mmm) cc_final: 0.8671 (mmp) REVERT: F 23 PHE cc_start: 0.7825 (m-80) cc_final: 0.6874 (t80) REVERT: H 1 MET cc_start: 0.3276 (OUTLIER) cc_final: 0.3002 (ttt) REVERT: H 32 SER cc_start: 0.8439 (t) cc_final: 0.8170 (t) REVERT: B 176 LEU cc_start: 0.7946 (mp) cc_final: 0.7692 (tt) REVERT: B 197 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 488 ASP cc_start: 0.8434 (m-30) cc_final: 0.8123 (m-30) REVERT: B 669 MET cc_start: 0.4531 (ttm) cc_final: 0.4258 (ttp) REVERT: B 676 MET cc_start: 0.6341 (ttm) cc_final: 0.6140 (ttp) REVERT: B 706 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8019 (pt0) REVERT: B 737 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8430 (mttp) REVERT: B 892 MET cc_start: 0.8915 (mmm) cc_final: 0.8685 (mmp) REVERT: C 23 PHE cc_start: 0.7790 (m-80) cc_final: 0.6826 (t80) REVERT: D 1 MET cc_start: 0.3078 (OUTLIER) cc_final: 0.2782 (ttt) REVERT: D 80 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8074 (mp) REVERT: E 174 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 176 LEU cc_start: 0.8030 (mp) cc_final: 0.7721 (tt) REVERT: E 183 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7345 (mmtm) REVERT: E 197 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7375 (tm-30) REVERT: E 306 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8696 (m) REVERT: G 23 PHE cc_start: 0.7857 (m-80) cc_final: 0.6992 (t80) REVERT: I 32 SER cc_start: 0.8303 (t) cc_final: 0.8070 (t) outliers start: 49 outliers final: 16 residues processed: 319 average time/residue: 0.7155 time to fit residues: 256.3990 Evaluate side-chains 279 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 3.9990 chunk 213 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 244 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3718 r_free = 0.3718 target = 0.139318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111565 restraints weight = 25660.834| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.78 r_work: 0.3303 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21462 Z= 0.125 Angle : 0.526 9.112 28980 Z= 0.267 Chirality : 0.041 0.157 3372 Planarity : 0.004 0.031 3582 Dihedral : 15.030 140.971 3694 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.27 % Allowed : 12.43 % Favored : 85.30 % 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: 0.74 (0.16), residues: 2643 helix: 0.96 (0.12), residues: 1794 sheet: 0.03 (0.40), residues: 156 loop : -0.39 (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 0.023 0.001 PHE A 438 TRP 0.008 0.001 TRP B 936 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00289 (21459) covalent geometry : angle 0.52556 (28980) hydrogen bonds : bond 0.03786 ( 1377) hydrogen bonds : angle 4.03634 ( 3996) Misc. bond : bond 0.00102 ( 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 327 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.815 Fit side-chains REVERT: A 176 LEU cc_start: 0.7844 (mp) cc_final: 0.7537 (tt) REVERT: A 197 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7577 (tm-30) REVERT: F 23 PHE cc_start: 0.7811 (m-80) cc_final: 0.6909 (t80) REVERT: H 1 MET cc_start: 0.3356 (OUTLIER) cc_final: 0.3048 (ttt) REVERT: H 32 SER cc_start: 0.8555 (t) cc_final: 0.8310 (t) REVERT: B 111 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7359 (tp40) REVERT: B 176 LEU cc_start: 0.7919 (mp) cc_final: 0.7644 (tt) REVERT: B 197 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7580 (tm-30) REVERT: B 488 ASP cc_start: 0.8396 (m-30) cc_final: 0.8018 (m-30) REVERT: B 676 MET cc_start: 0.6366 (ttm) cc_final: 0.6153 (ttp) REVERT: B 706 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8031 (pt0) REVERT: B 737 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8413 (mttp) REVERT: B 892 MET cc_start: 0.8945 (mmm) cc_final: 0.8734 (mmp) REVERT: C 23 PHE cc_start: 0.7820 (m-80) cc_final: 0.6867 (t80) REVERT: D 1 MET cc_start: 0.2707 (OUTLIER) cc_final: 0.2335 (ttt) REVERT: D 32 SER cc_start: 0.8580 (t) cc_final: 0.7954 (p) REVERT: E 174 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7479 (mt-10) REVERT: E 176 LEU cc_start: 0.7964 (mp) cc_final: 0.7666 (tt) REVERT: E 197 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7388 (tm-30) REVERT: G 23 PHE cc_start: 0.7849 (m-80) cc_final: 0.7000 (t80) REVERT: I 32 SER cc_start: 0.8370 (t) cc_final: 0.7525 (p) outliers start: 48 outliers final: 17 residues processed: 307 average time/residue: 0.7088 time to fit residues: 244.9082 Evaluate side-chains 281 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 111 GLN 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 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 417 ASP 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 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: 4.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 157 GLN E 111 GLN E 414 ASN E 494 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.137177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109070 restraints weight = 25808.266| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.79 r_work: 0.3263 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21462 Z= 0.185 Angle : 0.573 10.019 28980 Z= 0.290 Chirality : 0.044 0.166 3372 Planarity : 0.004 0.032 3582 Dihedral : 14.806 138.059 3690 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.74 % Allowed : 13.14 % Favored : 84.11 % 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: 0.95 (0.16), residues: 2643 helix: 1.13 (0.12), residues: 1770 sheet: 0.24 (0.39), residues: 156 loop : -0.35 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 796 TYR 0.009 0.001 TYR A 300 PHE 0.027 0.002 PHE A 438 TRP 0.012 0.002 TRP B 379 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00447 (21459) covalent geometry : angle 0.57262 (28980) hydrogen bonds : bond 0.04208 ( 1377) hydrogen bonds : angle 4.10479 ( 3996) Misc. bond : bond 0.00157 ( 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 317 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 0.810 Fit side-chains REVERT: A 176 LEU cc_start: 0.7878 (mp) cc_final: 0.7529 (tt) REVERT: A 197 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7640 (tm-30) REVERT: F 23 PHE cc_start: 0.7835 (m-80) cc_final: 0.6893 (t80) REVERT: H 1 MET cc_start: 0.3270 (OUTLIER) cc_final: 0.2997 (ttt) REVERT: B 176 LEU cc_start: 0.7898 (mp) cc_final: 0.7647 (tt) REVERT: B 197 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 488 ASP cc_start: 0.8452 (m-30) cc_final: 0.8041 (m-30) REVERT: B 676 MET cc_start: 0.6356 (ttm) cc_final: 0.6091 (ttp) REVERT: B 706 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8038 (pt0) REVERT: B 737 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8390 (mttp) REVERT: B 892 MET cc_start: 0.8944 (mmm) cc_final: 0.8736 (mmp) REVERT: C 23 PHE cc_start: 0.7830 (m-80) cc_final: 0.6849 (t80) REVERT: D 32 SER cc_start: 0.8616 (t) cc_final: 0.8012 (p) REVERT: E 174 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7560 (mt-10) REVERT: E 176 LEU cc_start: 0.8014 (mp) cc_final: 0.7651 (tt) REVERT: E 197 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7421 (tm-30) REVERT: E 224 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7518 (mtt180) REVERT: G 23 PHE cc_start: 0.7847 (m-80) cc_final: 0.6969 (t80) REVERT: I 32 SER cc_start: 0.8529 (t) cc_final: 0.7682 (p) outliers start: 58 outliers final: 20 residues processed: 295 average time/residue: 0.7136 time to fit residues: 236.7530 Evaluate side-chains 282 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 H residue 80 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 773 THR 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 224 ARG Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 769 SER 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: 0.8980 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 157 GLN B 157 GLN E 111 GLN E 157 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110648 restraints weight = 25596.479| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.78 r_work: 0.3286 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1761 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= 0.141 Angle : 0.536 9.501 28980 Z= 0.272 Chirality : 0.042 0.172 3372 Planarity : 0.004 0.032 3582 Dihedral : 14.351 134.706 3690 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.46 % Allowed : 13.71 % Favored : 83.83 % 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: 1.27 (0.16), residues: 2643 helix: 1.36 (0.12), residues: 1770 sheet: 0.37 (0.39), residues: 156 loop : -0.18 (0.24), residues: 717 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 0.022 0.001 PHE B 438 TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00335 (21459) covalent geometry : angle 0.53584 (28980) hydrogen bonds : bond 0.03850 ( 1377) hydrogen bonds : angle 3.99310 ( 3996) Misc. bond : bond 0.00093 ( 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 321 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 0.779 Fit side-chains REVERT: A 157 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7410 (tp-100) REVERT: A 176 LEU cc_start: 0.7890 (mp) cc_final: 0.7535 (tt) REVERT: A 197 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 224 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7476 (mtt180) REVERT: A 429 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7757 (mm-30) REVERT: F 23 PHE cc_start: 0.7842 (m-80) cc_final: 0.6914 (t80) REVERT: H 1 MET cc_start: 0.3318 (ttt) cc_final: 0.3061 (ttt) REVERT: H 30 GLU cc_start: 0.8205 (pm20) cc_final: 0.7840 (pm20) REVERT: H 32 SER cc_start: 0.8563 (t) cc_final: 0.8130 (p) REVERT: B 76 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7923 (mptm) REVERT: B 111 GLN cc_start: 0.7869 (tt0) cc_final: 0.7563 (tp40) REVERT: B 176 LEU cc_start: 0.7894 (mp) cc_final: 0.7621 (tt) REVERT: B 197 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 488 ASP cc_start: 0.8418 (m-30) cc_final: 0.7989 (m-30) REVERT: B 676 MET cc_start: 0.6357 (ttm) cc_final: 0.6088 (ttp) REVERT: B 706 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7996 (pt0) REVERT: B 737 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8399 (mttp) REVERT: B 892 MET cc_start: 0.8952 (mmm) cc_final: 0.8752 (mmp) REVERT: C 23 PHE cc_start: 0.7839 (m-80) cc_final: 0.6885 (t80) REVERT: D 32 SER cc_start: 0.8678 (t) cc_final: 0.8117 (p) REVERT: D 80 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8019 (mp) REVERT: E 76 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8038 (mtpt) REVERT: E 157 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7545 (tp-100) REVERT: E 174 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7497 (mt-10) REVERT: E 176 LEU cc_start: 0.7889 (mp) cc_final: 0.7600 (tt) REVERT: E 197 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7446 (tm-30) REVERT: E 224 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7484 (mtt180) REVERT: G 23 PHE cc_start: 0.7862 (m-80) cc_final: 0.7004 (t80) REVERT: I 32 SER cc_start: 0.8593 (t) cc_final: 0.7762 (p) outliers start: 52 outliers final: 22 residues processed: 300 average time/residue: 0.7076 time to fit residues: 238.9098 Evaluate side-chains 284 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 224 ARG 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 H residue 28 THR Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 773 THR 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 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 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 769 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 215 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 157 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 = 0.3703 r_free = 0.3703 target = 0.138296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109962 restraints weight = 25577.051| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.83 r_work: 0.3283 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21462 Z= 0.115 Angle : 0.518 8.386 28980 Z= 0.262 Chirality : 0.041 0.201 3372 Planarity : 0.004 0.031 3582 Dihedral : 13.957 131.454 3690 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.41 % Allowed : 14.56 % Favored : 83.03 % 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: 1.54 (0.17), residues: 2643 helix: 1.53 (0.12), residues: 1779 sheet: 0.55 (0.41), residues: 156 loop : -0.00 (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 E 109 PHE 0.020 0.001 PHE B 438 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00265 (21459) covalent geometry : angle 0.51821 (28980) hydrogen bonds : bond 0.03600 ( 1377) hydrogen bonds : angle 3.92860 ( 3996) Misc. bond : bond 0.00051 ( 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: 51 poor density : 271 time to evaluate : 0.785 Fit side-chains REVERT: A 176 LEU cc_start: 0.7851 (mp) cc_final: 0.7531 (tt) REVERT: A 197 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 224 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7421 (mtt180) REVERT: A 429 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 703 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7637 (ttt90) REVERT: F 1 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6448 (tmm) REVERT: F 23 PHE cc_start: 0.7771 (m-80) cc_final: 0.6869 (t80) REVERT: H 1 MET cc_start: 0.3216 (OUTLIER) cc_final: 0.2976 (ttt) REVERT: H 30 GLU cc_start: 0.8148 (pm20) cc_final: 0.7835 (pm20) REVERT: H 32 SER cc_start: 0.8489 (t) cc_final: 0.8050 (p) REVERT: H 80 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8186 (mp) REVERT: B 76 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7888 (mptm) REVERT: B 111 GLN cc_start: 0.7832 (tt0) cc_final: 0.7504 (tp40) REVERT: B 176 LEU cc_start: 0.7897 (mp) cc_final: 0.7595 (tt) REVERT: B 197 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 488 ASP cc_start: 0.8459 (m-30) cc_final: 0.7972 (m-30) REVERT: B 669 MET cc_start: 0.3938 (ttm) cc_final: 0.3725 (ttp) REVERT: B 676 MET cc_start: 0.6230 (ttm) cc_final: 0.5975 (ttp) REVERT: B 706 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7945 (pt0) REVERT: B 737 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8374 (mttp) REVERT: B 892 MET cc_start: 0.8932 (mmm) cc_final: 0.8732 (mmp) REVERT: C 23 PHE cc_start: 0.7811 (m-80) cc_final: 0.6866 (t80) REVERT: D 32 SER cc_start: 0.8657 (t) cc_final: 0.8114 (p) REVERT: E 76 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8016 (mtpt) REVERT: E 174 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7473 (mt-10) REVERT: E 176 LEU cc_start: 0.7855 (mp) cc_final: 0.7538 (tt) REVERT: E 197 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7447 (tm-30) REVERT: E 224 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7486 (mtt180) REVERT: G 23 PHE cc_start: 0.7846 (m-80) cc_final: 0.6963 (t80) REVERT: I 30 GLU cc_start: 0.8129 (pm20) cc_final: 0.7914 (pm20) REVERT: I 32 SER cc_start: 0.8599 (t) cc_final: 0.7772 (p) outliers start: 51 outliers final: 31 residues processed: 298 average time/residue: 0.6867 time to fit residues: 230.1156 Evaluate side-chains 297 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 141 SER 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 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 37 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 709 LEU 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 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 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 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: 0.9990 chunk 121 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 244 optimal weight: 0.5980 chunk 158 optimal weight: 0.5980 chunk 133 optimal weight: 0.0000 chunk 117 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 157 GLN B 494 HIS E 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111186 restraints weight = 25488.775| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.83 r_work: 0.3298 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21462 Z= 0.108 Angle : 0.504 6.929 28980 Z= 0.255 Chirality : 0.041 0.210 3372 Planarity : 0.004 0.030 3582 Dihedral : 13.407 125.327 3690 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.36 % Allowed : 15.32 % Favored : 82.32 % 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: 1.79 (0.17), residues: 2643 helix: 1.66 (0.12), residues: 1791 sheet: 0.66 (0.41), residues: 156 loop : 0.24 (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 B 109 PHE 0.019 0.001 PHE B 438 TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS E 437 Details of bonding type rmsd covalent geometry : bond 0.00250 (21459) covalent geometry : angle 0.50379 (28980) hydrogen bonds : bond 0.03412 ( 1377) hydrogen bonds : angle 3.84687 ( 3996) Misc. bond : bond 0.00040 ( 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 324 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 0.766 Fit side-chains REVERT: A 176 LEU cc_start: 0.7825 (mp) cc_final: 0.7524 (tt) REVERT: A 197 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A 224 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7436 (mtt180) REVERT: A 429 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7584 (mm-30) REVERT: F 1 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6367 (tmm) REVERT: F 23 PHE cc_start: 0.7724 (m-80) cc_final: 0.6825 (t80) REVERT: H 1 MET cc_start: 0.3046 (ttt) cc_final: 0.2813 (ttt) REVERT: H 30 GLU cc_start: 0.8113 (pm20) cc_final: 0.7799 (pm20) REVERT: H 32 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8026 (p) REVERT: H 80 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 76 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7861 (mptm) REVERT: B 111 GLN cc_start: 0.7749 (tt0) cc_final: 0.7386 (tp40) REVERT: B 176 LEU cc_start: 0.7886 (mp) cc_final: 0.7581 (tt) REVERT: B 197 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 429 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 488 ASP cc_start: 0.8431 (m-30) cc_final: 0.7924 (m-30) REVERT: B 676 MET cc_start: 0.6170 (ttm) cc_final: 0.5928 (ttp) REVERT: B 706 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7950 (pt0) REVERT: B 737 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8394 (mttp) REVERT: B 892 MET cc_start: 0.8906 (mmm) cc_final: 0.8706 (mmp) REVERT: C 23 PHE cc_start: 0.7811 (m-80) cc_final: 0.6857 (t80) REVERT: D 32 SER cc_start: 0.8638 (t) cc_final: 0.8063 (p) REVERT: E 76 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8031 (mtpt) REVERT: E 174 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7525 (mt-10) REVERT: E 176 LEU cc_start: 0.7855 (mp) cc_final: 0.7563 (tt) REVERT: E 197 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7402 (tm-30) REVERT: E 224 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7411 (mtt180) REVERT: E 429 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7595 (mm-30) REVERT: E 773 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8282 (p) REVERT: G 23 PHE cc_start: 0.7818 (m-80) cc_final: 0.6931 (t80) REVERT: I 32 SER cc_start: 0.8501 (t) cc_final: 0.7710 (p) outliers start: 50 outliers final: 30 residues processed: 302 average time/residue: 0.7041 time to fit residues: 239.4235 Evaluate side-chains 295 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 32 SER 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 438 PHE Chi-restraints excluded: chain B residue 709 LEU 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 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 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 Chi-restraints excluded: chain I residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 0.0050 chunk 15 optimal weight: 7.9990 chunk 241 optimal weight: 0.9980 chunk 236 optimal weight: 0.6980 chunk 180 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 192 optimal weight: 0.0870 chunk 225 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 941 GLN B 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113302 restraints weight = 25369.540| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.83 r_work: 0.3320 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21462 Z= 0.101 Angle : 0.495 6.545 28980 Z= 0.251 Chirality : 0.040 0.191 3372 Planarity : 0.003 0.036 3582 Dihedral : 12.879 118.131 3690 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.22 % Allowed : 15.65 % Favored : 82.13 % 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: 2.02 (0.17), residues: 2643 helix: 1.87 (0.12), residues: 1776 sheet: 0.72 (0.42), residues: 156 loop : 0.25 (0.25), residues: 711 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 0.018 0.001 PHE B 438 TRP 0.007 0.001 TRP A 936 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00230 (21459) covalent geometry : angle 0.49540 (28980) hydrogen bonds : bond 0.03234 ( 1377) hydrogen bonds : angle 3.78061 ( 3996) Misc. bond : bond 0.00029 ( 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 324 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.799 Fit side-chains REVERT: A 176 LEU cc_start: 0.7797 (mp) cc_final: 0.7516 (tt) REVERT: A 197 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 224 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7370 (mtt180) REVERT: A 429 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7536 (mm-30) REVERT: F 1 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6196 (tmm) REVERT: F 23 PHE cc_start: 0.7603 (m-80) cc_final: 0.6710 (t80) REVERT: H 1 MET cc_start: 0.2850 (ttt) cc_final: 0.2485 (ttt) REVERT: H 30 GLU cc_start: 0.8058 (pm20) cc_final: 0.7709 (pm20) REVERT: H 32 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.7949 (p) REVERT: H 53 ASP cc_start: 0.8761 (m-30) cc_final: 0.8555 (m-30) REVERT: H 79 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7617 (mttt) REVERT: B 76 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7812 (mptm) REVERT: B 111 GLN cc_start: 0.7733 (tt0) cc_final: 0.7369 (tp40) REVERT: B 176 LEU cc_start: 0.7879 (mp) cc_final: 0.7576 (tt) REVERT: B 197 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 429 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 488 ASP cc_start: 0.8394 (m-30) cc_final: 0.7853 (m-30) REVERT: B 676 MET cc_start: 0.6116 (ttm) cc_final: 0.5882 (ttp) REVERT: B 706 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7843 (pt0) REVERT: B 737 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8367 (mttp) REVERT: B 892 MET cc_start: 0.8878 (mmm) cc_final: 0.8672 (mmp) REVERT: C 23 PHE cc_start: 0.7767 (m-80) cc_final: 0.6823 (t80) REVERT: D 32 SER cc_start: 0.8614 (t) cc_final: 0.7978 (p) REVERT: D 68 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7779 (ttp80) REVERT: E 76 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7978 (mtpt) REVERT: E 95 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7971 (pt) REVERT: E 111 GLN cc_start: 0.7938 (tp40) cc_final: 0.7619 (tp40) REVERT: E 176 LEU cc_start: 0.7886 (mp) cc_final: 0.7543 (tt) REVERT: E 197 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7336 (tm-30) REVERT: E 224 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7391 (mtt180) REVERT: E 429 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 773 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8284 (p) REVERT: G 23 PHE cc_start: 0.7760 (m-80) cc_final: 0.6889 (t80) REVERT: I 32 SER cc_start: 0.8524 (t) cc_final: 0.7769 (p) outliers start: 47 outliers final: 31 residues processed: 304 average time/residue: 0.6910 time to fit residues: 236.5109 Evaluate side-chains 298 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain H residue 32 SER 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 709 LEU 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 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 224 ARG Chi-restraints excluded: chain E residue 331 TYR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 127 optimal weight: 0.0570 chunk 259 optimal weight: 0.0770 chunk 245 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 157 GLN E 941 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114207 restraints weight = 25421.032| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.83 r_work: 0.3291 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21462 Z= 0.097 Angle : 0.489 6.610 28980 Z= 0.248 Chirality : 0.040 0.195 3372 Planarity : 0.003 0.030 3582 Dihedral : 12.545 113.509 3690 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.08 % Allowed : 15.74 % Favored : 82.17 % 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: 2.17 (0.17), residues: 2643 helix: 1.97 (0.12), residues: 1782 sheet: 0.74 (0.43), residues: 156 loop : 0.35 (0.25), residues: 705 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 0.020 0.001 PHE A 261 TRP 0.007 0.001 TRP A 936 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00218 (21459) covalent geometry : angle 0.48891 (28980) hydrogen bonds : bond 0.03145 ( 1377) hydrogen bonds : angle 3.74255 ( 3996) Misc. bond : bond 0.00015 ( 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 321 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.796 Fit side-chains REVERT: A 111 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7382 (tp-100) REVERT: A 197 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 224 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7346 (mtt180) REVERT: A 429 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7552 (mm-30) REVERT: F 1 MET cc_start: 0.6686 (tmt) cc_final: 0.6327 (tmm) REVERT: F 23 PHE cc_start: 0.7807 (m-80) cc_final: 0.6995 (t80) REVERT: H 1 MET cc_start: 0.2845 (ttt) cc_final: 0.2501 (ttt) REVERT: H 30 GLU cc_start: 0.8081 (pm20) cc_final: 0.7769 (pm20) REVERT: H 32 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8091 (p) REVERT: H 79 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7784 (mttt) REVERT: B 76 LYS cc_start: 0.8381 (mtpt) cc_final: 0.7999 (mptm) REVERT: B 111 GLN cc_start: 0.7816 (tt0) cc_final: 0.7488 (tp40) REVERT: B 157 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7514 (tp-100) REVERT: B 176 LEU cc_start: 0.7865 (mp) cc_final: 0.7595 (tt) REVERT: B 197 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7412 (tm-30) REVERT: B 429 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7444 (mm-30) REVERT: B 440 GLN cc_start: 0.7110 (pt0) cc_final: 0.6784 (pt0) REVERT: B 488 ASP cc_start: 0.8396 (m-30) cc_final: 0.7877 (m-30) REVERT: B 676 MET cc_start: 0.6211 (ttm) cc_final: 0.5972 (ttp) REVERT: B 737 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8478 (mttp) REVERT: B 892 MET cc_start: 0.8955 (mmm) cc_final: 0.8745 (mmp) REVERT: C 23 PHE cc_start: 0.7886 (m-80) cc_final: 0.7061 (t80) REVERT: D 32 SER cc_start: 0.8716 (t) cc_final: 0.8101 (p) REVERT: D 68 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7816 (ttp80) REVERT: E 76 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8135 (mtpt) REVERT: E 111 GLN cc_start: 0.7969 (tp40) cc_final: 0.7668 (tp40) REVERT: E 176 LEU cc_start: 0.7897 (mp) cc_final: 0.7580 (tt) REVERT: E 197 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7410 (tm-30) REVERT: E 224 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7320 (mtt180) REVERT: E 773 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8400 (p) REVERT: G 23 PHE cc_start: 0.7879 (m-80) cc_final: 0.7147 (t80) REVERT: I 32 SER cc_start: 0.8595 (t) cc_final: 0.7925 (p) outliers start: 44 outliers final: 29 residues processed: 304 average time/residue: 0.7062 time to fit residues: 241.8685 Evaluate side-chains 301 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 H residue 28 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 709 LEU 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 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 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 417 ASP 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 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 494 HIS E 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111803 restraints weight = 25611.678| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.84 r_work: 0.3260 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2246 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= 0.124 Angle : 0.510 6.877 28980 Z= 0.259 Chirality : 0.041 0.198 3372 Planarity : 0.004 0.030 3582 Dihedral : 12.556 112.210 3690 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.65 % Allowed : 16.41 % Favored : 81.94 % 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: 2.13 (0.17), residues: 2643 helix: 1.94 (0.12), residues: 1773 sheet: 0.85 (0.42), residues: 156 loop : 0.32 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 796 TYR 0.011 0.001 TYR A 109 PHE 0.026 0.001 PHE E 438 TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00295 (21459) covalent geometry : angle 0.51043 (28980) hydrogen bonds : bond 0.03397 ( 1377) hydrogen bonds : angle 3.80679 ( 3996) Misc. bond : bond 0.00074 ( 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 299 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.786 Fit side-chains REVERT: A 111 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7254 (tp-100) REVERT: A 197 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 224 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7399 (mtt180) REVERT: A 429 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7601 (mm-30) REVERT: F 1 MET cc_start: 0.6704 (tmt) cc_final: 0.6352 (tmm) REVERT: F 23 PHE cc_start: 0.7833 (m-80) cc_final: 0.7014 (t80) REVERT: H 1 MET cc_start: 0.2661 (ttt) cc_final: 0.2319 (ttt) REVERT: H 30 GLU cc_start: 0.8111 (pm20) cc_final: 0.7792 (pm20) REVERT: H 32 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8110 (p) REVERT: H 53 ASP cc_start: 0.8507 (m-30) cc_final: 0.8302 (m-30) REVERT: H 79 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7790 (mttt) REVERT: B 76 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8033 (mptm) REVERT: B 111 GLN cc_start: 0.7823 (tt0) cc_final: 0.7486 (tp40) REVERT: B 176 LEU cc_start: 0.7930 (mp) cc_final: 0.7637 (tt) REVERT: B 197 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 429 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7471 (mm-30) REVERT: B 440 GLN cc_start: 0.7185 (pt0) cc_final: 0.6710 (pt0) REVERT: B 488 ASP cc_start: 0.8430 (m-30) cc_final: 0.7952 (m-30) REVERT: B 676 MET cc_start: 0.6211 (ttm) cc_final: 0.5976 (ttp) REVERT: B 737 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8485 (mttp) REVERT: C 23 PHE cc_start: 0.7905 (m-80) cc_final: 0.7066 (t80) REVERT: D 32 SER cc_start: 0.8710 (t) cc_final: 0.8117 (p) REVERT: D 68 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7803 (ttp80) REVERT: E 76 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8152 (mtpt) REVERT: E 111 GLN cc_start: 0.8001 (tp40) cc_final: 0.7696 (tp40) REVERT: E 176 LEU cc_start: 0.7906 (mp) cc_final: 0.7575 (tt) REVERT: E 197 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 224 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7397 (mtt180) REVERT: G 23 PHE cc_start: 0.7897 (m-80) cc_final: 0.7119 (t80) REVERT: I 32 SER cc_start: 0.8674 (t) cc_final: 0.7991 (p) outliers start: 35 outliers final: 29 residues processed: 285 average time/residue: 0.6949 time to fit residues: 223.2350 Evaluate side-chains 295 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 H residue 28 THR Chi-restraints excluded: chain H residue 32 SER 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 773 THR Chi-restraints excluded: chain B residue 860 GLU 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 121 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 417 ASP 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 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: 1.9990 chunk 88 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 216 optimal weight: 0.0020 chunk 207 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112189 restraints weight = 25553.756| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.84 r_work: 0.3298 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2241 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= 0.119 Angle : 0.511 6.736 28980 Z= 0.259 Chirality : 0.041 0.196 3372 Planarity : 0.004 0.030 3582 Dihedral : 12.521 110.856 3690 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.80 % Allowed : 16.31 % Favored : 81.89 % 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: 2.12 (0.17), residues: 2643 helix: 1.92 (0.12), residues: 1776 sheet: 0.86 (0.42), residues: 156 loop : 0.35 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 796 TYR 0.010 0.001 TYR B 331 PHE 0.025 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 covalent geometry : bond 0.00282 (21459) covalent geometry : angle 0.51102 (28980) hydrogen bonds : bond 0.03429 ( 1377) hydrogen bonds : angle 3.80943 ( 3996) Misc. bond : bond 0.00060 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7811.57 seconds wall clock time: 133 minutes 43.33 seconds (8023.33 seconds total)