Starting phenix.real_space_refine on Sat Jul 4 18:42:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e9f_31030/07_2026/7e9f_31030.cif" } resolution = 4.0 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= 0.001 sd= 0.003 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 12591 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 249 5.49 5 S 4 5.16 5 C 7588 2.51 5 N 2468 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13279 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 734 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 781 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2506 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2600 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "K" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1221 Unusual residues: {'ACE': 1} Classifications: {'peptide': 163, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "L" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1221 Unusual residues: {'ACE': 1} Classifications: {'peptide': 163, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 3.01, per 1000 atoms: 0.23 Number of scatterers: 13279 At special positions: 0 Unit cell: (113, 116, 116, 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 4 16.00 P 249 15.00 O 2970 8.00 N 2468 7.00 C 7588 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=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 510.7 milliseconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 55.5% alpha, 8.7% beta 117 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.609A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.596A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.745A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.623A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.530A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.308A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.526A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'D' and resid 40 through 49 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.542A pdb=" N LYS D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 107 through 127 removed outlier: 3.872A pdb=" N LYS D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.871A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.335A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.595A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.336A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.617A pdb=" N ASN G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.580A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 86 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.552A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 126 removed outlier: 3.574A pdb=" N LYS H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 30 Processing helix chain 'K' and resid 189 through 199 removed outlier: 4.403A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 212 removed outlier: 3.596A pdb=" N ALA K 204 " --> pdb=" O GLU K 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR K 212 " --> pdb=" O LEU K 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 189 through 199 removed outlier: 4.402A pdb=" N ALA L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 212 removed outlier: 3.597A pdb=" N ALA L 204 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU L 206 " --> pdb=" O ARG L 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR L 212 " --> pdb=" O LEU L 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.577A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.557A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.388A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.018A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain 'K' and resid 146 through 149 removed outlier: 5.857A pdb=" N PHE K 146 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS K 59 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG K 148 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL K 68 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 85 " --> pdb=" O ALA K 139 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA K 139 " --> pdb=" O LEU K 85 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA K 87 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU K 137 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR K 89 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR K 133 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG K 174 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU K 134 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE K 176 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALA K 136 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'L' and resid 146 through 149 removed outlier: 5.857A pdb=" N PHE L 146 " --> pdb=" O HIS L 59 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS L 59 " --> pdb=" O PHE L 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG L 148 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL L 68 " --> pdb=" O TYR L 90 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP L 86 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU L 74 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU L 85 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA L 139 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA L 87 " --> pdb=" O GLU L 137 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU L 137 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR L 89 " --> pdb=" O THR L 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR L 133 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG L 174 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU L 134 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE L 176 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ALA L 136 " --> pdb=" O ILE L 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2644 1.33 - 1.45: 4127 1.45 - 1.57: 6732 1.57 - 1.69: 496 1.69 - 1.81: 6 Bond restraints: 14005 Sorted by residual: bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C3' DC I 54 " pdb=" C2' DC I 54 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA I 103 " pdb=" C2' DA I 103 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" C1' DT J 45 " pdb=" N1 DT J 45 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.34e+00 bond pdb=" C5' DA I 39 " pdb=" C4' DA I 39 " ideal model delta sigma weight residual 1.512 1.533 -0.021 7.00e-03 2.04e+04 8.90e+00 ... (remaining 14000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 18967 1.91 - 3.82: 968 3.82 - 5.73: 53 5.73 - 7.64: 13 7.64 - 9.55: 6 Bond angle restraints: 20007 Sorted by residual: angle pdb=" O4' DT I 27 " pdb=" C4' DT I 27 " pdb=" C3' DT I 27 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.83e+01 angle pdb=" O4' DG J 130 " pdb=" C4' DG J 130 " pdb=" C3' DG J 130 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O4' DT J 107 " pdb=" C4' DT J 107 " pdb=" C3' DT J 107 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 68 " pdb=" C4 DT I 68 " pdb=" O4 DT I 68 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 20002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.38: 5977 29.38 - 58.77: 1609 58.77 - 88.15: 137 88.15 - 117.54: 1 117.54 - 146.92: 2 Dihedral angle restraints: 7726 sinusoidal: 4661 harmonic: 3065 Sorted by residual: dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 73.08 146.92 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DG I 63 " pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " pdb=" P DC I 64 " ideal model delta sinusoidal sigma weight residual 220.00 77.94 142.06 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" CA GLU B 74 " pdb=" C GLU B 74 " pdb=" N HIS B 75 " pdb=" CA HIS B 75 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 7723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1526 0.040 - 0.081: 576 0.081 - 0.121: 187 0.121 - 0.161: 21 0.161 - 0.201: 6 Chirality restraints: 2316 Sorted by residual: chirality pdb=" P DG I 25 " pdb=" OP1 DG I 25 " pdb=" OP2 DG I 25 " pdb=" O5' DG I 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.54 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 2313 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 32 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO E 66 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO G 81 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " -0.028 5.00e-02 4.00e+02 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3030 2.79 - 3.32: 10791 3.32 - 3.85: 26708 3.85 - 4.37: 28995 4.37 - 4.90: 42896 Nonbonded interactions: 112420 Sorted by model distance: nonbonded pdb=" O2 DC I 130 " pdb=" N2 DG J 18 " model vdw 2.264 2.496 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.319 2.496 nonbonded pdb=" OG SER H 93 " pdb=" OE1 GLU H 96 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN G 42 " pdb=" OG SER H 90 " model vdw 2.376 3.040 nonbonded pdb=" OG SER D 67 " pdb=" O GLY F 101 " model vdw 2.387 3.040 ... (remaining 112415 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 46 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 132)) selection = (chain 'E' and (resid 46 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 132)) } ncs_group { reference = (chain 'B' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116)) selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 116)) } ncs_group { reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 127)) selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 127)) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.005 0.055 14005 Z= 0.481 Angle : 0.857 9.548 20007 Z= 0.713 Chirality : 0.046 0.201 2316 Planarity : 0.005 0.066 1668 Dihedral : 28.022 146.923 5742 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.36 % Allowed : 6.89 % Favored : 92.74 % 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: -4.61 (0.18), residues: 1029 helix: -2.87 (0.14), residues: 567 sheet: -3.24 (0.54), residues: 44 loop : -3.14 (0.22), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.009 0.001 TYR K 40 PHE 0.024 0.002 PHE H 68 TRP 0.009 0.001 TRP K 93 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.48 (14005) covalent geometry : angle 0.85664 / 0.71 (20007) hydrogen bonds : bond 0.13623 / 9.10 ( 722) hydrogen bonds : angle 5.82274 / 3.95 ( 1821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 377 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8660 (mt) cc_final: 0.7930 (mp) REVERT: A 79 LYS cc_start: 0.8434 (tptm) cc_final: 0.8182 (tptp) REVERT: A 92 LEU cc_start: 0.9163 (mt) cc_final: 0.8861 (tp) REVERT: B 25 ASN cc_start: 0.8257 (m-40) cc_final: 0.8037 (m110) REVERT: B 35 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8008 (ttm110) REVERT: B 37 LEU cc_start: 0.9502 (mt) cc_final: 0.9119 (mt) REVERT: B 52 GLU cc_start: 0.8229 (tp30) cc_final: 0.7969 (tp30) REVERT: B 77 LYS cc_start: 0.8849 (mttt) cc_final: 0.8512 (mttm) REVERT: C 26 PHE cc_start: 0.8908 (m-80) cc_final: 0.8344 (m-10) REVERT: C 43 ARG cc_start: 0.8717 (mtp180) cc_final: 0.8452 (mtp-110) REVERT: C 53 THR cc_start: 0.8791 (m) cc_final: 0.8570 (m) REVERT: C 96 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8555 (ttmt) REVERT: D 46 LYS cc_start: 0.9348 (ttmt) cc_final: 0.9125 (ttmm) REVERT: D 79 GLU cc_start: 0.8327 (tp30) cc_final: 0.7725 (tp30) REVERT: E 54 PHE cc_start: 0.7397 (m-80) cc_final: 0.6547 (m-10) REVERT: E 69 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7828 (ptp90) REVERT: F 40 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7776 (ttt180) REVERT: F 83 SER cc_start: 0.8232 (p) cc_final: 0.8021 (m) REVERT: G 39 ASN cc_start: 0.8404 (m-40) cc_final: 0.8088 (p0) REVERT: H 43 TYR cc_start: 0.7620 (m-80) cc_final: 0.7174 (m-80) REVERT: H 46 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9120 (ttmm) REVERT: H 86 TYR cc_start: 0.7918 (m-10) cc_final: 0.7561 (m-10) REVERT: K 49 LYS cc_start: 0.6236 (mtmt) cc_final: 0.5394 (mmtp) REVERT: L 49 LYS cc_start: 0.6371 (mtmt) cc_final: 0.5668 (mmtp) REVERT: L 79 LEU cc_start: 0.7380 (mt) cc_final: 0.6588 (mp) REVERT: L 134 LEU cc_start: 0.7157 (mt) cc_final: 0.6932 (tt) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.1674 time to fit residues: 82.5837 Evaluate side-chains 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 32 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS F 25 ASN G 74 ASN K 145 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.120076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086861 restraints weight = 41466.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089087 restraints weight = 24576.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090552 restraints weight = 18011.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091405 restraints weight = 15212.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091833 restraints weight = 13917.101| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14005 Z= 0.182 Angle : 0.737 11.044 20007 Z= 0.408 Chirality : 0.050 0.230 2316 Planarity : 0.007 0.098 1668 Dihedral : 31.602 151.160 3864 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.08 % Allowed : 20.44 % Favored : 74.49 % 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: -2.74 (0.22), residues: 1029 helix: -1.19 (0.18), residues: 577 sheet: -2.90 (0.58), residues: 40 loop : -2.53 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 40 TYR 0.016 0.002 TYR L 40 PHE 0.012 0.002 PHE D 68 TRP 0.022 0.004 TRP K 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (14005) covalent geometry : angle 0.73673 / 0.41 (20007) hydrogen bonds : bond 0.05324 / 3.70 ( 722) hydrogen bonds : angle 4.29038 / 2.92 ( 1821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7890 (mttt) cc_final: 0.7603 (mttm) REVERT: A 79 LYS cc_start: 0.8440 (tptm) cc_final: 0.8227 (tptp) REVERT: A 97 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 35 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.8090 (ttm110) REVERT: B 40 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7948 (ttp80) REVERT: B 52 GLU cc_start: 0.7874 (tp30) cc_final: 0.7630 (tp30) REVERT: B 95 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8318 (ttm-80) REVERT: C 26 PHE cc_start: 0.8994 (m-80) cc_final: 0.8656 (m-10) REVERT: C 96 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8673 (ttmt) REVERT: C 100 ASN cc_start: 0.8097 (p0) cc_final: 0.7721 (p0) REVERT: D 86 TYR cc_start: 0.8044 (m-10) cc_final: 0.7535 (m-10) REVERT: E 54 PHE cc_start: 0.7500 (m-80) cc_final: 0.6729 (m-10) REVERT: E 59 GLU cc_start: 0.8468 (pm20) cc_final: 0.8138 (pm20) REVERT: E 69 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.7896 (ptp90) REVERT: E 123 ASP cc_start: 0.8348 (m-30) cc_final: 0.8081 (t0) REVERT: F 35 ARG cc_start: 0.8485 (ttm110) cc_final: 0.7858 (ttm110) REVERT: F 52 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7444 (tp30) REVERT: F 70 VAL cc_start: 0.8899 (t) cc_final: 0.8689 (p) REVERT: F 83 SER cc_start: 0.8817 (p) cc_final: 0.8389 (t) REVERT: G 39 ASN cc_start: 0.7881 (m-40) cc_final: 0.7675 (m110) REVERT: K 49 LYS cc_start: 0.6180 (mtmt) cc_final: 0.5444 (mmtp) REVERT: L 49 LYS cc_start: 0.6273 (mtmt) cc_final: 0.5715 (mmtp) REVERT: L 148 ARG cc_start: 0.6470 (ptt-90) cc_final: 0.5954 (pmt170) outliers start: 42 outliers final: 29 residues processed: 295 average time/residue: 0.1554 time to fit residues: 60.7394 Evaluate side-chains 249 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN K 27 GLN L 59 HIS L 145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.117676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084147 restraints weight = 41732.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.086275 restraints weight = 24708.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087658 restraints weight = 18255.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088311 restraints weight = 15526.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088852 restraints weight = 14363.383| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14005 Z= 0.197 Angle : 0.706 8.558 20007 Z= 0.394 Chirality : 0.048 0.208 2316 Planarity : 0.005 0.092 1668 Dihedral : 31.597 151.247 3864 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 6.17 % Allowed : 22.61 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1029 helix: -0.30 (0.20), residues: 576 sheet: -2.31 (0.66), residues: 40 loop : -2.21 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 43 TYR 0.029 0.002 TYR F 88 PHE 0.008 0.002 PHE F 61 TRP 0.018 0.004 TRP K 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (14005) covalent geometry : angle 0.70595 / 0.39 (20007) hydrogen bonds : bond 0.05288 / 3.65 ( 722) hydrogen bonds : angle 4.24606 / 2.90 ( 1821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8345 (pm20) cc_final: 0.8123 (pm20) REVERT: B 25 ASN cc_start: 0.8432 (m-40) cc_final: 0.7985 (m110) REVERT: B 35 ARG cc_start: 0.8616 (mtp-110) cc_final: 0.8185 (ttm110) REVERT: B 40 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8220 (mmm-85) REVERT: B 95 ARG cc_start: 0.8834 (ttm-80) cc_final: 0.8369 (ttm-80) REVERT: C 26 PHE cc_start: 0.9121 (m-80) cc_final: 0.8670 (m-10) REVERT: C 96 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8635 (ttmt) REVERT: C 100 ASN cc_start: 0.7713 (p0) cc_final: 0.7455 (p0) REVERT: D 74 GLU cc_start: 0.8665 (tt0) cc_final: 0.8398 (tt0) REVERT: D 86 TYR cc_start: 0.8123 (m-10) cc_final: 0.7632 (m-10) REVERT: E 54 PHE cc_start: 0.7443 (m-80) cc_final: 0.6868 (m-10) REVERT: E 59 GLU cc_start: 0.8444 (pm20) cc_final: 0.8092 (pm20) REVERT: E 69 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8081 (ptp90) REVERT: E 73 GLU cc_start: 0.7836 (tt0) cc_final: 0.6999 (tt0) REVERT: E 123 ASP cc_start: 0.8558 (m-30) cc_final: 0.8224 (t0) REVERT: F 25 ASN cc_start: 0.8371 (m110) cc_final: 0.7574 (m110) REVERT: F 35 ARG cc_start: 0.8556 (ttm110) cc_final: 0.7940 (ttm110) REVERT: F 40 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8091 (tpp80) REVERT: F 52 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7607 (tp30) REVERT: F 74 GLU cc_start: 0.8514 (tt0) cc_final: 0.8309 (tt0) REVERT: F 83 SER cc_start: 0.8719 (p) cc_final: 0.8204 (t) REVERT: G 82 ARG cc_start: 0.8833 (tpt-90) cc_final: 0.8584 (tpt-90) REVERT: H 72 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8941 (tp) REVERT: K 40 TYR cc_start: 0.4955 (p90) cc_final: 0.4664 (p90) REVERT: K 79 LEU cc_start: 0.7320 (mt) cc_final: 0.6362 (mp) REVERT: L 49 LYS cc_start: 0.6329 (mtmt) cc_final: 0.5606 (mmtp) REVERT: L 86 TRP cc_start: 0.6966 (m-90) cc_final: 0.6709 (m-90) outliers start: 51 outliers final: 40 residues processed: 275 average time/residue: 0.1354 time to fit residues: 50.6936 Evaluate side-chains 250 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 124 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 50.0000 chunk 45 optimal weight: 0.8980 chunk 119 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.117697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084414 restraints weight = 41388.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086547 restraints weight = 24550.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087945 restraints weight = 18098.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088749 restraints weight = 15367.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.089097 restraints weight = 14098.705| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14005 Z= 0.161 Angle : 0.672 10.394 20007 Z= 0.376 Chirality : 0.046 0.204 2316 Planarity : 0.005 0.078 1668 Dihedral : 31.543 151.788 3864 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.65 % Allowed : 25.15 % Favored : 68.20 % 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: -1.15 (0.25), residues: 1029 helix: 0.25 (0.21), residues: 576 sheet: -1.85 (0.73), residues: 40 loop : -2.11 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 174 TYR 0.029 0.002 TYR F 88 PHE 0.011 0.001 PHE D 68 TRP 0.014 0.002 TRP K 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (14005) covalent geometry : angle 0.67160 / 0.38 (20007) hydrogen bonds : bond 0.04852 / 3.39 ( 722) hydrogen bonds : angle 4.10289 / 2.80 ( 1821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8396 (m-40) cc_final: 0.7985 (m110) REVERT: B 35 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8109 (ttm-80) REVERT: B 40 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7902 (ttp80) REVERT: B 95 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8363 (ttm-80) REVERT: C 43 ARG cc_start: 0.8657 (mtp180) cc_final: 0.8076 (mtp85) REVERT: C 74 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8144 (t0) REVERT: C 96 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8618 (ttmt) REVERT: C 100 ASN cc_start: 0.7900 (p0) cc_final: 0.7551 (p0) REVERT: D 86 TYR cc_start: 0.8042 (m-10) cc_final: 0.7557 (m-10) REVERT: E 54 PHE cc_start: 0.7471 (m-80) cc_final: 0.7017 (m-10) REVERT: E 59 GLU cc_start: 0.8442 (pm20) cc_final: 0.8136 (pm20) REVERT: E 69 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8113 (ptp90) REVERT: E 73 GLU cc_start: 0.7684 (tt0) cc_final: 0.7308 (tt0) REVERT: E 123 ASP cc_start: 0.8388 (m-30) cc_final: 0.8161 (t0) REVERT: F 40 ARG cc_start: 0.8452 (tpp80) cc_final: 0.7804 (tpp80) REVERT: F 52 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7637 (tp30) REVERT: F 83 SER cc_start: 0.8676 (p) cc_final: 0.8241 (t) REVERT: F 84 LEU cc_start: 0.9119 (tp) cc_final: 0.8812 (tp) REVERT: K 79 LEU cc_start: 0.7142 (mt) cc_final: 0.6454 (mp) REVERT: K 86 TRP cc_start: 0.6814 (m-90) cc_final: 0.6445 (m-90) REVERT: L 40 TYR cc_start: 0.5074 (p90) cc_final: 0.4743 (p90) REVERT: L 73 GLU cc_start: 0.7472 (mp0) cc_final: 0.7268 (mp0) REVERT: L 86 TRP cc_start: 0.7011 (m-90) cc_final: 0.6658 (m-90) outliers start: 55 outliers final: 40 residues processed: 262 average time/residue: 0.1432 time to fit residues: 51.4350 Evaluate side-chains 248 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 77 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 105 optimal weight: 0.0020 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.118623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085484 restraints weight = 41139.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.087510 restraints weight = 24568.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.088867 restraints weight = 18342.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089662 restraints weight = 15696.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.090067 restraints weight = 14424.516| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14005 Z= 0.138 Angle : 0.649 10.113 20007 Z= 0.364 Chirality : 0.045 0.208 2316 Planarity : 0.004 0.051 1668 Dihedral : 31.436 151.980 3864 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 6.29 % Allowed : 25.63 % Favored : 68.08 % 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: -0.85 (0.25), residues: 1029 helix: 0.47 (0.21), residues: 580 sheet: -1.46 (0.77), residues: 40 loop : -1.97 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 35 TYR 0.020 0.001 TYR F 88 PHE 0.014 0.001 PHE G 26 TRP 0.011 0.001 TRP K 86 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (14005) covalent geometry : angle 0.64915 / 0.36 (20007) hydrogen bonds : bond 0.04641 / 3.27 ( 722) hydrogen bonds : angle 3.97217 / 2.70 ( 1821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8499 (m-40) cc_final: 0.8133 (m110) REVERT: B 40 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7877 (ttp80) REVERT: B 77 LYS cc_start: 0.8815 (mttt) cc_final: 0.8430 (mttp) REVERT: C 26 PHE cc_start: 0.9125 (m-80) cc_final: 0.8913 (m-80) REVERT: C 74 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8175 (t0) REVERT: C 100 ASN cc_start: 0.7848 (p0) cc_final: 0.7529 (p0) REVERT: D 86 TYR cc_start: 0.8024 (m-10) cc_final: 0.7611 (m-10) REVERT: E 54 PHE cc_start: 0.7434 (m-80) cc_final: 0.6992 (m-10) REVERT: E 59 GLU cc_start: 0.8408 (pm20) cc_final: 0.8129 (pm20) REVERT: E 73 GLU cc_start: 0.7747 (tt0) cc_final: 0.6712 (tt0) REVERT: F 25 ASN cc_start: 0.8314 (m110) cc_final: 0.7311 (m110) REVERT: F 34 ILE cc_start: 0.9375 (mm) cc_final: 0.9122 (mm) REVERT: F 40 ARG cc_start: 0.8520 (tpp80) cc_final: 0.8045 (tpp80) REVERT: F 52 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7601 (tp30) REVERT: F 83 SER cc_start: 0.8620 (p) cc_final: 0.8132 (t) REVERT: F 84 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8615 (tp) REVERT: F 88 TYR cc_start: 0.8361 (m-10) cc_final: 0.8108 (m-80) REVERT: G 56 LEU cc_start: 0.8636 (pp) cc_final: 0.8397 (tp) REVERT: K 75 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7505 (ptp-170) REVERT: K 86 TRP cc_start: 0.6933 (m-90) cc_final: 0.6437 (m-90) REVERT: L 40 TYR cc_start: 0.5383 (p90) cc_final: 0.4826 (p90) outliers start: 52 outliers final: 38 residues processed: 261 average time/residue: 0.1394 time to fit residues: 49.7678 Evaluate side-chains 250 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 9 optimal weight: 0.0070 chunk 119 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 93 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS G 74 ASN ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.117950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084437 restraints weight = 41512.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086516 restraints weight = 24550.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087933 restraints weight = 18192.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.088707 restraints weight = 15456.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089044 restraints weight = 14214.445| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14005 Z= 0.158 Angle : 0.664 9.028 20007 Z= 0.370 Chirality : 0.045 0.209 2316 Planarity : 0.004 0.049 1668 Dihedral : 31.370 152.149 3864 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.77 % Allowed : 26.84 % Favored : 66.38 % 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: -0.68 (0.25), residues: 1029 helix: 0.58 (0.21), residues: 580 sheet: -1.28 (0.80), residues: 40 loop : -1.88 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 69 TYR 0.015 0.001 TYR F 88 PHE 0.013 0.002 PHE H 68 TRP 0.004 0.001 TRP L 11 HIS 0.004 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (14005) covalent geometry : angle 0.66406 / 0.37 (20007) hydrogen bonds : bond 0.04784 / 3.33 ( 722) hydrogen bonds : angle 3.97974 / 2.71 ( 1821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8507 (m-40) cc_final: 0.8119 (m110) REVERT: B 35 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.8467 (ttm-80) REVERT: B 40 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7808 (ttp80) REVERT: B 44 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8486 (mttm) REVERT: B 77 LYS cc_start: 0.8868 (mttt) cc_final: 0.8513 (mttp) REVERT: C 74 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8198 (t0) REVERT: C 100 ASN cc_start: 0.7941 (p0) cc_final: 0.7604 (p0) REVERT: D 86 TYR cc_start: 0.8034 (m-10) cc_final: 0.7533 (m-10) REVERT: E 54 PHE cc_start: 0.7297 (m-80) cc_final: 0.6938 (m-10) REVERT: E 59 GLU cc_start: 0.8445 (pm20) cc_final: 0.8229 (pm20) REVERT: E 69 ARG cc_start: 0.8178 (ptp90) cc_final: 0.7806 (ptp90) REVERT: E 70 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8024 (tp) REVERT: E 73 GLU cc_start: 0.7820 (tt0) cc_final: 0.6697 (tt0) REVERT: E 129 ARG cc_start: 0.8210 (tpt-90) cc_final: 0.7692 (ttp80) REVERT: F 25 ASN cc_start: 0.8239 (m110) cc_final: 0.7160 (m110) REVERT: F 52 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7635 (tp30) REVERT: F 83 SER cc_start: 0.8626 (p) cc_final: 0.8184 (t) REVERT: F 84 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8427 (tp) REVERT: F 88 TYR cc_start: 0.8414 (m-10) cc_final: 0.8075 (m-80) REVERT: G 56 LEU cc_start: 0.8631 (pp) cc_final: 0.8347 (tp) REVERT: K 75 ARG cc_start: 0.7959 (ptp-170) cc_final: 0.7507 (ptp-170) REVERT: K 79 LEU cc_start: 0.6976 (mt) cc_final: 0.6054 (mp) REVERT: K 86 TRP cc_start: 0.6761 (m-90) cc_final: 0.6176 (m-90) REVERT: L 40 TYR cc_start: 0.5369 (p90) cc_final: 0.4829 (p90) REVERT: L 86 TRP cc_start: 0.6981 (m-90) cc_final: 0.6582 (m-90) outliers start: 56 outliers final: 39 residues processed: 257 average time/residue: 0.1382 time to fit residues: 48.7359 Evaluate side-chains 254 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.116044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082606 restraints weight = 40888.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.084522 restraints weight = 24684.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085808 restraints weight = 18572.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086411 restraints weight = 15921.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.086887 restraints weight = 14798.148| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14005 Z= 0.213 Angle : 0.713 9.574 20007 Z= 0.390 Chirality : 0.047 0.212 2316 Planarity : 0.005 0.047 1668 Dihedral : 31.388 151.958 3864 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 7.62 % Allowed : 26.00 % Favored : 66.38 % 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: -0.79 (0.26), residues: 1029 helix: 0.47 (0.21), residues: 580 sheet: -1.20 (0.61), residues: 66 loop : -1.92 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 53 TYR 0.022 0.002 TYR D 43 PHE 0.020 0.002 PHE G 26 TRP 0.005 0.001 TRP L 11 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (14005) covalent geometry : angle 0.71288 / 0.39 (20007) hydrogen bonds : bond 0.05350 / 3.68 ( 722) hydrogen bonds : angle 4.13961 / 2.82 ( 1821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7962 (ttp80) REVERT: B 46 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8632 (mm) REVERT: C 74 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8206 (t0) REVERT: C 100 ASN cc_start: 0.7945 (p0) cc_final: 0.7642 (p0) REVERT: D 86 TYR cc_start: 0.8089 (m-10) cc_final: 0.7588 (m-10) REVERT: E 73 GLU cc_start: 0.7877 (tt0) cc_final: 0.7282 (tt0) REVERT: F 40 ARG cc_start: 0.8494 (tpp80) cc_final: 0.8092 (tpp80) REVERT: F 52 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7715 (tp30) REVERT: F 83 SER cc_start: 0.8788 (p) cc_final: 0.8342 (t) REVERT: G 59 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8375 (tp) REVERT: G 82 ARG cc_start: 0.8702 (tpt-90) cc_final: 0.8307 (tpt90) REVERT: G 86 LEU cc_start: 0.9572 (mt) cc_final: 0.8734 (mt) REVERT: K 40 TYR cc_start: 0.5345 (p90) cc_final: 0.5003 (p90) REVERT: K 75 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7713 (ptp-170) REVERT: K 86 TRP cc_start: 0.6922 (m-90) cc_final: 0.6589 (m-90) REVERT: L 40 TYR cc_start: 0.5356 (p90) cc_final: 0.4977 (p90) REVERT: L 133 TYR cc_start: 0.4939 (OUTLIER) cc_final: 0.4310 (m-80) outliers start: 63 outliers final: 47 residues processed: 253 average time/residue: 0.1416 time to fit residues: 49.3776 Evaluate side-chains 251 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 40.0000 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 57 optimal weight: 0.1980 chunk 116 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.118496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085148 restraints weight = 40465.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087148 restraints weight = 24233.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088460 restraints weight = 18171.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.089209 restraints weight = 15603.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089517 restraints weight = 14438.399| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14005 Z= 0.142 Angle : 0.672 10.138 20007 Z= 0.374 Chirality : 0.046 0.214 2316 Planarity : 0.004 0.051 1668 Dihedral : 31.332 151.849 3864 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.72 % Allowed : 28.66 % Favored : 66.63 % 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: -0.55 (0.26), residues: 1029 helix: 0.67 (0.22), residues: 579 sheet: -1.24 (0.79), residues: 40 loop : -1.79 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 119 TYR 0.019 0.002 TYR H 43 PHE 0.018 0.002 PHE G 26 TRP 0.003 0.001 TRP L 86 HIS 0.005 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (14005) covalent geometry : angle 0.67230 / 0.37 (20007) hydrogen bonds : bond 0.04667 / 3.28 ( 722) hydrogen bonds : angle 3.88959 / 2.64 ( 1821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8507 (m-40) cc_final: 0.8142 (m110) REVERT: B 40 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: B 77 LYS cc_start: 0.8767 (mttt) cc_final: 0.8431 (mttp) REVERT: C 100 ASN cc_start: 0.7990 (p0) cc_final: 0.7704 (p0) REVERT: D 86 TYR cc_start: 0.8038 (m-10) cc_final: 0.7554 (m-10) REVERT: D 116 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 73 GLU cc_start: 0.7893 (tt0) cc_final: 0.6685 (tt0) REVERT: E 129 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7743 (ttp80) REVERT: F 25 ASN cc_start: 0.8300 (m110) cc_final: 0.7097 (m110) REVERT: F 34 ILE cc_start: 0.9357 (mm) cc_final: 0.9114 (mm) REVERT: F 52 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7540 (tp30) REVERT: F 75 HIS cc_start: 0.9125 (OUTLIER) cc_final: 0.8535 (t70) REVERT: F 83 SER cc_start: 0.8609 (p) cc_final: 0.8084 (t) REVERT: F 84 LEU cc_start: 0.8957 (tp) cc_final: 0.8752 (tp) REVERT: F 85 ASP cc_start: 0.8667 (p0) cc_final: 0.8419 (p0) REVERT: G 59 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8455 (tp) REVERT: G 82 ARG cc_start: 0.8614 (tpt-90) cc_final: 0.8274 (tpt90) REVERT: H 43 TYR cc_start: 0.8087 (m-80) cc_final: 0.7774 (m-10) REVERT: H 95 ARG cc_start: 0.8212 (mtm110) cc_final: 0.7780 (mtp85) REVERT: K 75 ARG cc_start: 0.7966 (ptp-170) cc_final: 0.7666 (ptp-170) REVERT: K 86 TRP cc_start: 0.6863 (m-90) cc_final: 0.6515 (m-90) REVERT: L 40 TYR cc_start: 0.5453 (p90) cc_final: 0.4976 (p90) REVERT: L 86 TRP cc_start: 0.7037 (m-90) cc_final: 0.6648 (m-90) REVERT: L 193 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8533 (mmmm) outliers start: 39 outliers final: 29 residues processed: 246 average time/residue: 0.1389 time to fit residues: 46.6712 Evaluate side-chains 245 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 88 optimal weight: 40.0000 chunk 72 optimal weight: 40.0000 chunk 91 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.116446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082922 restraints weight = 41025.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084988 restraints weight = 24458.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086318 restraints weight = 18117.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.087040 restraints weight = 15488.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087374 restraints weight = 14321.516| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14005 Z= 0.201 Angle : 0.718 12.698 20007 Z= 0.393 Chirality : 0.047 0.212 2316 Planarity : 0.005 0.051 1668 Dihedral : 31.338 151.949 3864 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.32 % Allowed : 28.66 % Favored : 66.02 % 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 (0.25), residues: 1029 helix: 0.52 (0.21), residues: 580 sheet: -1.16 (0.60), residues: 66 loop : -1.93 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 119 TYR 0.019 0.002 TYR D 43 PHE 0.021 0.002 PHE G 26 TRP 0.004 0.001 TRP L 11 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (14005) covalent geometry : angle 0.71799 / 0.39 (20007) hydrogen bonds : bond 0.05264 / 3.62 ( 722) hydrogen bonds : angle 4.08353 / 2.78 ( 1821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: B 40 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7915 (ttp80) REVERT: B 44 LYS cc_start: 0.8475 (mttt) cc_final: 0.8261 (mttm) REVERT: B 46 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8743 (mt) REVERT: C 100 ASN cc_start: 0.8093 (p0) cc_final: 0.7771 (p0) REVERT: D 86 TYR cc_start: 0.8087 (m-10) cc_final: 0.7601 (m-10) REVERT: D 116 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7950 (tm-30) REVERT: E 73 GLU cc_start: 0.7951 (tt0) cc_final: 0.6702 (tt0) REVERT: E 129 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7971 (tpp80) REVERT: F 25 ASN cc_start: 0.8209 (m110) cc_final: 0.6961 (m-40) REVERT: F 52 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7658 (tp30) REVERT: F 75 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8592 (t70) REVERT: F 83 SER cc_start: 0.8749 (p) cc_final: 0.8448 (t) REVERT: F 85 ASP cc_start: 0.8898 (p0) cc_final: 0.8607 (p0) REVERT: G 59 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8491 (tp) REVERT: K 75 ARG cc_start: 0.8017 (ptp-170) cc_final: 0.7522 (ptp-170) REVERT: K 86 TRP cc_start: 0.6887 (m-90) cc_final: 0.6251 (m-90) REVERT: L 40 TYR cc_start: 0.5463 (p90) cc_final: 0.4892 (p90) REVERT: L 193 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8558 (mmmm) outliers start: 44 outliers final: 36 residues processed: 234 average time/residue: 0.1421 time to fit residues: 45.7569 Evaluate side-chains 235 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 2 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.117966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084866 restraints weight = 41371.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.086988 restraints weight = 24027.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.088378 restraints weight = 17627.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089177 restraints weight = 14949.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089524 restraints weight = 13720.411| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14005 Z= 0.141 Angle : 0.687 12.584 20007 Z= 0.381 Chirality : 0.046 0.221 2316 Planarity : 0.004 0.051 1668 Dihedral : 31.294 151.704 3864 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.99 % Allowed : 30.47 % Favored : 65.54 % 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: -0.52 (0.26), residues: 1029 helix: 0.69 (0.22), residues: 579 sheet: -0.82 (0.79), residues: 42 loop : -1.82 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 174 TYR 0.023 0.002 TYR H 86 PHE 0.019 0.002 PHE G 26 TRP 0.003 0.001 TRP K 86 HIS 0.005 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (14005) covalent geometry : angle 0.68699 / 0.38 (20007) hydrogen bonds : bond 0.04660 / 3.29 ( 722) hydrogen bonds : angle 3.91179 / 2.65 ( 1821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: B 77 LYS cc_start: 0.8831 (mttt) cc_final: 0.8474 (mttp) REVERT: C 26 PHE cc_start: 0.9112 (m-80) cc_final: 0.8867 (m-80) REVERT: C 100 ASN cc_start: 0.8054 (p0) cc_final: 0.7571 (p0) REVERT: D 86 TYR cc_start: 0.7983 (m-10) cc_final: 0.7555 (m-10) REVERT: D 116 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7911 (tm-30) REVERT: E 73 GLU cc_start: 0.7907 (tt0) cc_final: 0.6619 (tt0) REVERT: E 129 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7820 (ttp80) REVERT: F 25 ASN cc_start: 0.8194 (m110) cc_final: 0.6969 (m110) REVERT: F 34 ILE cc_start: 0.9399 (mm) cc_final: 0.9190 (mm) REVERT: F 75 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8210 (t70) REVERT: F 83 SER cc_start: 0.8651 (p) cc_final: 0.8167 (t) REVERT: F 85 ASP cc_start: 0.8866 (p0) cc_final: 0.8653 (p0) REVERT: G 59 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8550 (tp) REVERT: H 43 TYR cc_start: 0.8109 (m-80) cc_final: 0.7827 (m-10) REVERT: H 95 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7702 (mtm180) REVERT: K 75 ARG cc_start: 0.7991 (ptp-170) cc_final: 0.7540 (ptp-170) REVERT: K 86 TRP cc_start: 0.6816 (m-90) cc_final: 0.6228 (m-90) REVERT: L 40 TYR cc_start: 0.5374 (p90) cc_final: 0.4825 (p90) REVERT: L 79 LEU cc_start: 0.6732 (mt) cc_final: 0.5663 (mp) REVERT: L 193 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8543 (mmmm) outliers start: 33 outliers final: 27 residues processed: 240 average time/residue: 0.1435 time to fit residues: 47.0202 Evaluate side-chains 239 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.118362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085042 restraints weight = 40727.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087081 restraints weight = 24429.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088385 restraints weight = 18212.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089126 restraints weight = 15607.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.089517 restraints weight = 14413.161| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14005 Z= 0.143 Angle : 0.686 12.427 20007 Z= 0.380 Chirality : 0.045 0.214 2316 Planarity : 0.004 0.053 1668 Dihedral : 31.225 151.996 3864 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.11 % Allowed : 31.08 % Favored : 64.81 % 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: -0.48 (0.25), residues: 1029 helix: 0.67 (0.21), residues: 579 sheet: -0.69 (0.80), residues: 42 loop : -1.73 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 69 TYR 0.023 0.002 TYR F 88 PHE 0.016 0.002 PHE G 26 TRP 0.002 0.000 TRP L 93 HIS 0.003 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (14005) covalent geometry : angle 0.68580 / 0.38 (20007) hydrogen bonds : bond 0.04633 / 3.25 ( 722) hydrogen bonds : angle 3.91102 / 2.66 ( 1821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.86 seconds wall clock time: 44 minutes 0.63 seconds (2640.63 seconds total)