Starting phenix.real_space_refine on Sun Sep 13 10:37:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e9f_31030/09_2026/7e9f_31030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9f_31030/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7e9f_31030/09_2026/7e9f_31030.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e9f_31030/09_2026/7e9f_31030.cif" model { file = "/net/cci-nas-00/data/ceres_data/7e9f_31030/09_2026/7e9f_31030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9f_31030/09_2026/7e9f_31030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9f_31030/09_2026/7e9f_31030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9f_31030/09_2026/7e9f_31030.map" } 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-2.2.1-6174/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: 2.52, per 1000 atoms: 0.19 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: 1.00 Conformation dependent library (CDL) restraints added in 374.5 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: 1.52 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: 1.78 Time building geometry restraints manager: 1.33 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: 18937 1.91 - 3.82: 996 3.82 - 5.73: 55 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.050 ------------------------------------------------------------------------------- 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 : 0.864 9.548 20007 Z= 0.721 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 0.86407 / 0.72 (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 : 0.397 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 62 ILE cc_start: 0.8660 (mt) cc_final: 0.7931 (mp) REVERT: A 79 LYS cc_start: 0.8434 (tptm) cc_final: 0.8183 (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: 0.8038 (m110) REVERT: B 35 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8009 (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: 0.7968 (tp30) REVERT: B 77 LYS cc_start: 0.8849 (mttt) cc_final: 0.8514 (mttm) REVERT: C 26 PHE cc_start: 0.8908 (m-80) cc_final: 0.8370 (m-10) REVERT: C 53 THR cc_start: 0.8791 (m) cc_final: 0.8575 (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: 0.9126 (ttmm) REVERT: D 79 GLU cc_start: 0.8327 (tp30) cc_final: 0.7724 (tp30) REVERT: D 91 THR cc_start: 0.9066 (m) cc_final: 0.8846 (p) REVERT: E 54 PHE cc_start: 0.7397 (m-80) cc_final: 0.6548 (m-10) REVERT: E 69 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7829 (ptp90) REVERT: F 40 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7777 (ttt180) REVERT: F 83 SER cc_start: 0.8232 (p) cc_final: 0.8019 (m) REVERT: G 39 ASN cc_start: 0.8404 (m-40) cc_final: 0.8093 (p0) REVERT: H 86 TYR cc_start: 0.7918 (m-10) cc_final: 0.7558 (m-10) REVERT: K 49 LYS cc_start: 0.6236 (mtmt) cc_final: 0.5397 (mmtp) REVERT: L 49 LYS cc_start: 0.6371 (mtmt) cc_final: 0.5670 (mmtp) REVERT: L 79 LEU cc_start: 0.7380 (mt) cc_final: 0.6585 (mp) REVERT: L 134 LEU cc_start: 0.7157 (mt) cc_final: 0.6933 (tt) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.1594 time to fit residues: 78.9368 Evaluate side-chains 232 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.120746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087646 restraints weight = 41219.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089900 restraints weight = 24153.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.091380 restraints weight = 17645.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092220 restraints weight = 14879.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.092589 restraints weight = 13606.728| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14005 Z= 0.165 Angle : 0.729 11.052 20007 Z= 0.407 Chirality : 0.049 0.230 2316 Planarity : 0.006 0.062 1668 Dihedral : 31.529 149.817 3864 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.84 % Allowed : 19.83 % Favored : 75.33 % 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: -2.77 (0.22), residues: 1029 helix: -1.20 (0.18), residues: 577 sheet: -2.90 (0.57), residues: 40 loop : -2.57 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 75 TYR 0.015 0.002 TYR L 40 PHE 0.013 0.002 PHE D 68 TRP 0.010 0.003 TRP K 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (14005) covalent geometry : angle 0.72902 / 0.41 (20007) hydrogen bonds : bond 0.05310 / 3.70 ( 722) hydrogen bonds : angle 4.27326 / 2.91 ( 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 304 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.346 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: 0.7880 (mttt) cc_final: 0.7592 (mttm) REVERT: A 79 LYS cc_start: 0.8452 (tptm) cc_final: 0.8224 (tptp) REVERT: A 97 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 131 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8035 (ttm110) REVERT: B 35 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8083 (ttm110) REVERT: B 40 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: B 52 GLU cc_start: 0.7888 (tp30) cc_final: 0.7649 (tp30) REVERT: B 95 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8289 (ttm-80) REVERT: C 26 PHE cc_start: 0.9028 (m-80) cc_final: 0.8425 (m-10) REVERT: C 43 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8113 (mtp85) REVERT: C 96 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8661 (ttmt) REVERT: C 100 ASN cc_start: 0.8083 (p0) cc_final: 0.7548 (p0) REVERT: D 86 TYR cc_start: 0.8021 (m-10) cc_final: 0.7513 (m-10) REVERT: D 91 THR cc_start: 0.9180 (m) cc_final: 0.8739 (p) REVERT: E 54 PHE cc_start: 0.7535 (m-80) cc_final: 0.6816 (m-10) REVERT: E 59 GLU cc_start: 0.8445 (pm20) cc_final: 0.8110 (pm20) REVERT: E 69 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.7874 (ptp90) REVERT: F 35 ARG cc_start: 0.8482 (ttm110) cc_final: 0.7854 (ttm110) REVERT: F 83 SER cc_start: 0.8829 (p) cc_final: 0.8383 (t) REVERT: G 30 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7582 (ttm-80) REVERT: K 49 LYS cc_start: 0.6161 (mtmt) cc_final: 0.5424 (mmtp) REVERT: L 49 LYS cc_start: 0.6265 (mtmt) cc_final: 0.5716 (mmtp) REVERT: L 148 ARG cc_start: 0.6457 (ptt-90) cc_final: 0.5976 (pmt170) outliers start: 40 outliers final: 26 residues processed: 293 average time/residue: 0.1412 time to fit residues: 54.9027 Evaluate side-chains 244 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 79 optimal weight: 40.0000 chunk 26 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 28 optimal weight: 0.0170 chunk 11 optimal weight: 7.9990 overall best weight: 2.4182 ------------------------------------------------------------------------------- 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 L 59 HIS L 145 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.118612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085193 restraints weight = 41507.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087315 restraints weight = 24494.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088699 restraints weight = 18138.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089508 restraints weight = 15410.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089866 restraints weight = 14146.495| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14005 Z= 0.172 Angle : 0.695 8.681 20007 Z= 0.389 Chirality : 0.048 0.216 2316 Planarity : 0.005 0.089 1668 Dihedral : 31.464 150.021 3864 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.80 % Allowed : 21.77 % Favored : 72.43 % 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: -0.28 (0.20), residues: 576 sheet: -2.49 (0.61), residues: 40 loop : -2.23 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 43 TYR 0.031 0.002 TYR F 88 PHE 0.010 0.002 PHE D 68 TRP 0.019 0.003 TRP K 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (14005) covalent geometry : angle 0.69530 / 0.39 (20007) hydrogen bonds : bond 0.05054 / 3.51 ( 722) hydrogen bonds : angle 4.16338 / 2.84 ( 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: 48 poor density : 244 time to evaluate : 0.365 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 64 LYS cc_start: 0.7814 (mttt) cc_final: 0.7606 (mttm) REVERT: B 25 ASN cc_start: 0.8421 (m-40) cc_final: 0.7972 (m110) REVERT: B 35 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.8147 (ttm110) REVERT: B 40 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: B 77 LYS cc_start: 0.8964 (mttt) cc_final: 0.8578 (mttm) REVERT: B 95 ARG cc_start: 0.8796 (ttm-80) cc_final: 0.8326 (ttm-80) REVERT: C 26 PHE cc_start: 0.9078 (m-80) cc_final: 0.8591 (m-10) REVERT: C 74 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8119 (t0) REVERT: C 93 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 96 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8635 (ttmt) REVERT: C 100 ASN cc_start: 0.7783 (p0) cc_final: 0.7458 (p0) REVERT: D 74 GLU cc_start: 0.8679 (tt0) cc_final: 0.8457 (tt0) REVERT: D 86 TYR cc_start: 0.8071 (m-10) cc_final: 0.7559 (m-10) REVERT: D 91 THR cc_start: 0.8955 (m) cc_final: 0.8637 (p) REVERT: E 54 PHE cc_start: 0.7477 (m-80) cc_final: 0.6892 (m-10) REVERT: E 59 GLU cc_start: 0.8400 (pm20) cc_final: 0.8058 (pm20) REVERT: E 69 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8049 (ptp90) REVERT: E 73 GLU cc_start: 0.7681 (tt0) cc_final: 0.7353 (tt0) REVERT: F 35 ARG cc_start: 0.8558 (ttm110) cc_final: 0.7978 (ttm110) REVERT: F 40 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8071 (tpp80) REVERT: F 52 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7549 (tp30) REVERT: F 83 SER cc_start: 0.8690 (p) cc_final: 0.8175 (t) REVERT: G 30 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: G 82 ARG cc_start: 0.8810 (tpt-90) cc_final: 0.8572 (tpt-90) REVERT: K 49 LYS cc_start: 0.6263 (mtmt) cc_final: 0.5510 (mmtp) REVERT: L 40 TYR cc_start: 0.5051 (p90) cc_final: 0.4684 (p90) REVERT: L 73 GLU cc_start: 0.7395 (mp0) cc_final: 0.7157 (mp0) REVERT: L 86 TRP cc_start: 0.7010 (m-90) cc_final: 0.6573 (m-90) outliers start: 48 outliers final: 37 residues processed: 275 average time/residue: 0.1353 time to fit residues: 50.5091 Evaluate side-chains 251 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 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 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 101 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 123 ASP 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 124 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 97 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 83 optimal weight: 50.0000 chunk 45 optimal weight: 0.8980 chunk 119 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 74 ASN ** 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 = 0.4082 r_free = 0.4082 target = 0.119344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086015 restraints weight = 40821.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088023 restraints weight = 24560.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.089415 restraints weight = 18438.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090164 restraints weight = 15755.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090575 restraints weight = 14537.487| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14005 Z= 0.144 Angle : 0.669 10.587 20007 Z= 0.374 Chirality : 0.046 0.220 2316 Planarity : 0.004 0.049 1668 Dihedral : 31.379 150.431 3864 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.29 % Allowed : 24.79 % Favored : 68.92 % 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: -1.19 (0.25), residues: 1029 helix: 0.21 (0.21), residues: 580 sheet: -1.96 (0.70), residues: 40 loop : -2.14 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 43 TYR 0.024 0.002 TYR H 86 PHE 0.013 0.001 PHE H 68 TRP 0.004 0.001 TRP L 86 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (14005) covalent geometry : angle 0.66854 / 0.37 (20007) hydrogen bonds : bond 0.04707 / 3.32 ( 722) hydrogen bonds : angle 3.99869 / 2.71 ( 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 287 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.316 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: 0.8442 (m-40) cc_final: 0.8060 (m110) REVERT: B 40 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7926 (ttp80) REVERT: B 77 LYS cc_start: 0.8904 (mttt) cc_final: 0.8389 (mttp) REVERT: B 95 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8321 (ttm-80) REVERT: C 26 PHE cc_start: 0.9057 (m-80) cc_final: 0.8634 (m-10) REVERT: C 93 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7379 (mt-10) REVERT: C 96 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8510 (ttpt) REVERT: C 100 ASN cc_start: 0.7909 (p0) cc_final: 0.7541 (p0) REVERT: D 74 GLU cc_start: 0.8613 (tt0) cc_final: 0.8406 (tt0) REVERT: D 86 TYR cc_start: 0.8003 (m-10) cc_final: 0.7522 (m-10) REVERT: D 91 THR cc_start: 0.8861 (m) cc_final: 0.8557 (p) REVERT: E 54 PHE cc_start: 0.7479 (m-80) cc_final: 0.7044 (m-10) REVERT: E 59 GLU cc_start: 0.8338 (pm20) cc_final: 0.8089 (pm20) REVERT: E 69 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8024 (ptp90) REVERT: E 73 GLU cc_start: 0.7552 (tt0) cc_final: 0.7231 (tt0) REVERT: E 129 ARG cc_start: 0.7839 (ttt90) cc_final: 0.7500 (ttp80) REVERT: F 35 ARG cc_start: 0.8467 (ttm110) cc_final: 0.7962 (ttm110) REVERT: F 40 ARG cc_start: 0.8411 (tpp80) cc_final: 0.7936 (tpp80) REVERT: F 52 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7541 (tp30) REVERT: F 83 SER cc_start: 0.8641 (p) cc_final: 0.8252 (t) REVERT: F 84 LEU cc_start: 0.9060 (tp) cc_final: 0.8768 (tp) REVERT: G 30 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7543 (ttm-80) REVERT: G 56 LEU cc_start: 0.8620 (pp) cc_final: 0.8349 (tp) REVERT: H 45 TYR cc_start: 0.6800 (t80) cc_final: 0.6491 (t80) REVERT: K 49 LYS cc_start: 0.6312 (mtmt) cc_final: 0.5523 (mmtp) REVERT: K 79 LEU cc_start: 0.6949 (mt) cc_final: 0.6058 (mp) REVERT: L 40 TYR cc_start: 0.5415 (p90) cc_final: 0.4865 (p90) outliers start: 52 outliers final: 37 residues processed: 270 average time/residue: 0.1295 time to fit residues: 48.4527 Evaluate side-chains 253 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 40 ARG 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 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 E residue 123 ASP 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: 40.0000 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS G 74 ASN ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.118279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084958 restraints weight = 40798.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087008 restraints weight = 24460.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088335 restraints weight = 18197.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089112 restraints weight = 15546.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089455 restraints weight = 14304.395| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14005 Z= 0.152 Angle : 0.661 9.716 20007 Z= 0.370 Chirality : 0.046 0.224 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.288 150.620 3864 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.29 % Allowed : 25.51 % 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: -0.83 (0.25), residues: 1029 helix: 0.49 (0.22), residues: 580 sheet: -1.51 (0.76), residues: 40 loop : -1.98 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 40 TYR 0.018 0.001 TYR F 88 PHE 0.013 0.001 PHE H 68 TRP 0.003 0.001 TRP L 11 HIS 0.003 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (14005) covalent geometry : angle 0.66129 / 0.37 (20007) hydrogen bonds : bond 0.04732 / 3.31 ( 722) hydrogen bonds : angle 3.96636 / 2.69 ( 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 278 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 0.257 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 50 GLU cc_start: 0.7484 (pt0) cc_final: 0.7244 (tt0) REVERT: B 25 ASN cc_start: 0.8497 (m-40) cc_final: 0.8153 (m110) REVERT: B 40 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7894 (ttp80) REVERT: C 93 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 96 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8590 (ttmt) REVERT: C 100 ASN cc_start: 0.7899 (p0) cc_final: 0.7566 (p0) REVERT: D 86 TYR cc_start: 0.8070 (m-10) cc_final: 0.7543 (m-10) REVERT: D 91 THR cc_start: 0.8907 (m) cc_final: 0.8596 (p) REVERT: E 54 PHE cc_start: 0.7428 (m-80) cc_final: 0.7024 (m-10) REVERT: E 59 GLU cc_start: 0.8394 (pm20) cc_final: 0.8152 (pm20) REVERT: E 69 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8117 (mtp180) REVERT: E 73 GLU cc_start: 0.7720 (tt0) cc_final: 0.6723 (tt0) REVERT: E 129 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7584 (ttp80) REVERT: F 25 ASN cc_start: 0.8302 (m110) cc_final: 0.7373 (m110) REVERT: F 34 ILE cc_start: 0.9358 (mm) cc_final: 0.9081 (mm) REVERT: F 40 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8003 (tpp80) REVERT: F 52 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7611 (tp30) REVERT: F 74 GLU cc_start: 0.8423 (tt0) cc_final: 0.8046 (tt0) REVERT: F 83 SER cc_start: 0.8663 (p) cc_final: 0.8154 (t) REVERT: F 84 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8747 (tp) REVERT: F 90 LEU cc_start: 0.9364 (mt) cc_final: 0.9061 (mt) REVERT: G 56 LEU cc_start: 0.8660 (pp) cc_final: 0.8323 (tp) REVERT: K 49 LYS cc_start: 0.6208 (mtmt) cc_final: 0.5455 (mmtp) REVERT: L 40 TYR cc_start: 0.5397 (p90) cc_final: 0.4845 (p90) REVERT: L 79 LEU cc_start: 0.6911 (mt) cc_final: 0.5542 (mp) outliers start: 52 outliers final: 42 residues processed: 258 average time/residue: 0.1274 time to fit residues: 45.1738 Evaluate side-chains 252 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 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 70 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 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 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 123 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 93 optimal weight: 40.0000 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.118805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085627 restraints weight = 41382.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087691 restraints weight = 24893.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.089027 restraints weight = 18576.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089770 restraints weight = 15898.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090147 restraints weight = 14652.547| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3403 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= 0.149 Angle : 0.658 11.053 20007 Z= 0.367 Chirality : 0.045 0.226 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.233 150.559 3864 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.41 % Allowed : 26.36 % Favored : 67.23 % 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: -0.69 (0.25), residues: 1029 helix: 0.58 (0.22), residues: 580 sheet: -1.27 (0.79), residues: 40 loop : -1.90 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 35 TYR 0.043 0.002 TYR F 88 PHE 0.014 0.002 PHE H 68 TRP 0.003 0.001 TRP L 11 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (14005) covalent geometry : angle 0.65812 / 0.37 (20007) hydrogen bonds : bond 0.04665 / 3.27 ( 722) hydrogen bonds : angle 3.94108 / 2.67 ( 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: 53 poor density : 226 time to evaluate : 0.398 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: A 50 GLU cc_start: 0.7500 (pt0) cc_final: 0.7219 (tt0) REVERT: B 25 ASN cc_start: 0.8516 (m-40) cc_final: 0.8165 (m110) REVERT: B 40 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7910 (ttp80) REVERT: C 26 PHE cc_start: 0.8901 (m-80) cc_final: 0.8393 (m-10) REVERT: C 93 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7212 (mm-30) REVERT: C 96 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8631 (ttmt) REVERT: C 100 ASN cc_start: 0.7918 (p0) cc_final: 0.7582 (p0) REVERT: D 86 TYR cc_start: 0.8002 (m-10) cc_final: 0.7476 (m-10) REVERT: D 88 LYS cc_start: 0.8530 (mppt) cc_final: 0.8292 (mmtt) REVERT: D 91 THR cc_start: 0.8924 (m) cc_final: 0.8591 (p) REVERT: E 54 PHE cc_start: 0.7410 (m-80) cc_final: 0.6987 (m-10) REVERT: E 59 GLU cc_start: 0.8401 (pm20) cc_final: 0.8197 (pm20) REVERT: E 69 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8068 (mtp180) REVERT: E 70 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7975 (tp) REVERT: E 73 GLU cc_start: 0.7748 (tt0) cc_final: 0.6596 (tt0) REVERT: E 129 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7627 (ttp80) REVERT: F 25 ASN cc_start: 0.8240 (m110) cc_final: 0.7181 (m110) REVERT: F 34 ILE cc_start: 0.9366 (mm) cc_final: 0.9134 (mm) REVERT: F 52 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7591 (tp30) REVERT: F 74 GLU cc_start: 0.8494 (tt0) cc_final: 0.8172 (tt0) REVERT: F 83 SER cc_start: 0.8610 (p) cc_final: 0.8038 (t) REVERT: F 88 TYR cc_start: 0.8319 (m-80) cc_final: 0.8006 (m-80) REVERT: F 90 LEU cc_start: 0.9348 (mt) cc_final: 0.9066 (mt) REVERT: F 91 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8753 (ptmt) REVERT: G 56 LEU cc_start: 0.8603 (pp) cc_final: 0.8285 (tp) REVERT: K 49 LYS cc_start: 0.6192 (mtmt) cc_final: 0.5473 (mmtp) REVERT: L 40 TYR cc_start: 0.5345 (p90) cc_final: 0.4922 (p90) REVERT: L 79 LEU cc_start: 0.7056 (mt) cc_final: 0.5704 (mp) REVERT: L 86 TRP cc_start: 0.7112 (m-90) cc_final: 0.6671 (m-90) outliers start: 53 outliers final: 36 residues processed: 260 average time/residue: 0.1318 time to fit residues: 47.0883 Evaluate side-chains 255 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 131 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 54 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 D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 70 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 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: 50.0000 chunk 59 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 106 optimal weight: 50.0000 chunk 110 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.116217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082685 restraints weight = 41239.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.084567 restraints weight = 25304.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085846 restraints weight = 19147.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086544 restraints weight = 16491.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086910 restraints weight = 15281.545| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14005 Z= 0.220 Angle : 0.734 10.103 20007 Z= 0.398 Chirality : 0.048 0.230 2316 Planarity : 0.005 0.046 1668 Dihedral : 31.264 150.399 3864 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 6.05 % Allowed : 27.45 % Favored : 66.51 % 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: -0.90 (0.25), residues: 1029 helix: 0.37 (0.21), residues: 580 sheet: -1.25 (0.79), residues: 40 loop : -1.95 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 174 TYR 0.040 0.002 TYR F 88 PHE 0.017 0.002 PHE A 67 TRP 0.008 0.001 TRP L 11 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (14005) covalent geometry : angle 0.73370 / 0.40 (20007) hydrogen bonds : bond 0.05555 / 3.81 ( 722) hydrogen bonds : angle 4.16381 / 2.84 ( 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 264 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 0.387 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 83 ARG cc_start: 0.7805 (ptp-110) cc_final: 0.7543 (ptp-110) REVERT: B 40 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: B 44 LYS cc_start: 0.8765 (mttt) cc_final: 0.8541 (mmtp) REVERT: B 77 LYS cc_start: 0.8940 (mttt) cc_final: 0.8525 (mttp) REVERT: C 26 PHE cc_start: 0.9128 (m-80) cc_final: 0.8511 (m-10) REVERT: C 100 ASN cc_start: 0.8000 (p0) cc_final: 0.7702 (p0) REVERT: D 86 TYR cc_start: 0.8138 (m-10) cc_final: 0.7562 (m-10) REVERT: D 88 LYS cc_start: 0.8542 (mppt) cc_final: 0.8317 (mmtt) REVERT: D 91 THR cc_start: 0.8999 (m) cc_final: 0.8604 (p) REVERT: D 116 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7895 (tm-30) REVERT: E 69 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8136 (mtp180) REVERT: E 73 GLU cc_start: 0.7908 (tt0) cc_final: 0.7306 (tt0) REVERT: E 123 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8038 (t0) REVERT: F 52 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7683 (tp30) REVERT: F 83 SER cc_start: 0.8638 (p) cc_final: 0.8312 (t) REVERT: F 91 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8791 (tttm) REVERT: G 26 PHE cc_start: 0.8604 (m-10) cc_final: 0.8345 (m-10) REVERT: L 40 TYR cc_start: 0.5318 (p90) cc_final: 0.4836 (p90) REVERT: L 79 LEU cc_start: 0.7033 (mt) cc_final: 0.6733 (mt) outliers start: 50 outliers final: 39 residues processed: 252 average time/residue: 0.1238 time to fit residues: 43.5393 Evaluate side-chains 245 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 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 E residue 123 ASP 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 94 optimal weight: 50.0000 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** 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 = 0.4035 r_free = 0.4035 target = 0.116143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082648 restraints weight = 40422.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.084596 restraints weight = 24378.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085848 restraints weight = 18360.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086559 restraints weight = 15793.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086904 restraints weight = 14651.055| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14005 Z= 0.209 Angle : 0.726 11.268 20007 Z= 0.396 Chirality : 0.048 0.232 2316 Planarity : 0.005 0.047 1668 Dihedral : 31.292 150.132 3864 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.32 % Allowed : 27.69 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.25), residues: 1029 helix: 0.34 (0.21), residues: 580 sheet: -1.35 (0.78), residues: 40 loop : -1.98 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 53 TYR 0.034 0.002 TYR F 88 PHE 0.013 0.002 PHE H 68 TRP 0.008 0.001 TRP K 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (14005) covalent geometry : angle 0.72565 / 0.40 (20007) hydrogen bonds : bond 0.05229 / 3.60 ( 722) hydrogen bonds : angle 4.13561 / 2.82 ( 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 252 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.432 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: A 50 GLU cc_start: 0.7568 (pt0) cc_final: 0.7301 (tt0) REVERT: B 40 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8043 (ttp80) REVERT: B 44 LYS cc_start: 0.8779 (mttt) cc_final: 0.8554 (mmtp) REVERT: B 77 LYS cc_start: 0.8939 (mttt) cc_final: 0.8519 (mttp) REVERT: C 100 ASN cc_start: 0.8059 (p0) cc_final: 0.7647 (p0) REVERT: D 86 TYR cc_start: 0.8158 (m-10) cc_final: 0.7593 (m-10) REVERT: D 88 LYS cc_start: 0.8554 (mppt) cc_final: 0.8318 (mmtt) REVERT: D 116 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7942 (tm-30) REVERT: E 69 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8212 (mtp180) REVERT: E 73 GLU cc_start: 0.7933 (tt0) cc_final: 0.6717 (tt0) REVERT: E 123 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.8019 (t0) REVERT: F 25 ASN cc_start: 0.8322 (m110) cc_final: 0.6776 (m-40) REVERT: F 52 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7706 (tp30) REVERT: F 83 SER cc_start: 0.8608 (p) cc_final: 0.8209 (t) REVERT: F 91 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8708 (ptmt) REVERT: G 26 PHE cc_start: 0.8743 (m-10) cc_final: 0.8384 (m-10) REVERT: K 40 TYR cc_start: 0.5399 (p90) cc_final: 0.5059 (p90) REVERT: L 40 TYR cc_start: 0.5415 (p90) cc_final: 0.4873 (p90) outliers start: 44 outliers final: 37 residues processed: 239 average time/residue: 0.1476 time to fit residues: 48.6250 Evaluate side-chains 235 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 74 GLU 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 101 VAL 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 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 E residue 123 ASP 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 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 185 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 88 optimal weight: 40.0000 chunk 72 optimal weight: 40.0000 chunk 91 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** 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 = 0.4032 r_free = 0.4032 target = 0.115925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082397 restraints weight = 40495.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084347 restraints weight = 24353.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085578 restraints weight = 18340.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.086285 restraints weight = 15822.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086558 restraints weight = 14629.297| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14005 Z= 0.199 Angle : 0.722 13.501 20007 Z= 0.394 Chirality : 0.048 0.231 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.265 149.958 3864 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.08 % Allowed : 28.30 % 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: -0.87 (0.25), residues: 1029 helix: 0.42 (0.21), residues: 578 sheet: -0.85 (0.79), residues: 42 loop : -2.02 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 119 TYR 0.029 0.002 TYR F 88 PHE 0.015 0.002 PHE A 67 TRP 0.008 0.001 TRP K 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (14005) covalent geometry : angle 0.72209 / 0.39 (20007) hydrogen bonds : bond 0.05222 / 3.59 ( 722) hydrogen bonds : angle 4.11807 / 2.80 ( 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 243 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7594 (pt0) cc_final: 0.7310 (tt0) REVERT: B 40 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8067 (ttp80) REVERT: B 77 LYS cc_start: 0.8910 (mttt) cc_final: 0.8509 (mttp) REVERT: C 100 ASN cc_start: 0.8026 (p0) cc_final: 0.7665 (p0) REVERT: D 86 TYR cc_start: 0.8173 (m-10) cc_final: 0.7599 (m-10) REVERT: D 88 LYS cc_start: 0.8602 (mppt) cc_final: 0.8329 (mmtt) REVERT: E 69 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8217 (mtp180) REVERT: E 73 GLU cc_start: 0.7968 (tt0) cc_final: 0.7343 (tt0) REVERT: F 52 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7689 (tp30) REVERT: F 75 HIS cc_start: 0.9232 (OUTLIER) cc_final: 0.8683 (t70) REVERT: F 83 SER cc_start: 0.8648 (p) cc_final: 0.8123 (t) REVERT: G 26 PHE cc_start: 0.8789 (m-10) cc_final: 0.8451 (m-10) REVERT: L 40 TYR cc_start: 0.5441 (p90) cc_final: 0.4858 (p90) outliers start: 42 outliers final: 36 residues processed: 232 average time/residue: 0.1458 time to fit residues: 46.7055 Evaluate side-chains 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 131 ARG Chi-restraints excluded: chain B residue 40 ARG 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 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 101 VAL 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 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 F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.0370 chunk 87 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- 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** B 75 HIS ** F 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.118094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085186 restraints weight = 41071.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087229 restraints weight = 24290.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.088539 restraints weight = 18039.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.089312 restraints weight = 15403.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089620 restraints weight = 14209.165| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4066 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= 0.141 Angle : 0.681 12.343 20007 Z= 0.377 Chirality : 0.046 0.230 2316 Planarity : 0.004 0.050 1668 Dihedral : 31.186 149.896 3864 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.39 % Allowed : 30.11 % Favored : 66.51 % 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: -0.63 (0.26), residues: 1029 helix: 0.61 (0.22), residues: 577 sheet: -0.74 (0.80), residues: 42 loop : -1.87 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 119 TYR 0.026 0.002 TYR H 86 PHE 0.019 0.002 PHE H 68 TRP 0.005 0.001 TRP K 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (14005) covalent geometry : angle 0.68111 / 0.38 (20007) hydrogen bonds : bond 0.04707 / 3.31 ( 722) hydrogen bonds : angle 3.92918 / 2.67 ( 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 242 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.405 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 50 GLU cc_start: 0.7606 (pt0) cc_final: 0.7286 (tt0) REVERT: B 77 LYS cc_start: 0.8813 (mttt) cc_final: 0.8433 (mttp) REVERT: C 100 ASN cc_start: 0.7907 (p0) cc_final: 0.7691 (p0) REVERT: D 86 TYR cc_start: 0.8111 (m-10) cc_final: 0.7675 (m-10) REVERT: D 88 LYS cc_start: 0.8539 (mppt) cc_final: 0.8282 (mmtt) REVERT: E 69 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8114 (mtp180) REVERT: E 73 GLU cc_start: 0.7881 (tt0) cc_final: 0.7295 (tt0) REVERT: F 40 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7926 (mtp85) REVERT: F 75 HIS cc_start: 0.9164 (OUTLIER) cc_final: 0.8580 (t70) REVERT: F 83 SER cc_start: 0.8542 (p) cc_final: 0.7946 (t) REVERT: G 26 PHE cc_start: 0.8700 (m-10) cc_final: 0.8320 (m-10) REVERT: L 40 TYR cc_start: 0.5202 (p90) cc_final: 0.4749 (p90) outliers start: 28 outliers final: 24 residues processed: 235 average time/residue: 0.1388 time to fit residues: 45.8396 Evaluate side-chains 229 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 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 75 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR 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: 5.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 57 optimal weight: 0.0060 chunk 71 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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** ** F 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.118693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085501 restraints weight = 40964.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087479 restraints weight = 24683.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088751 restraints weight = 18565.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.089460 restraints weight = 15963.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089744 restraints weight = 14820.082| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14005 Z= 0.138 Angle : 0.678 12.314 20007 Z= 0.375 Chirality : 0.046 0.230 2316 Planarity : 0.004 0.054 1668 Dihedral : 31.103 150.223 3864 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.39 % Allowed : 30.96 % Favored : 65.66 % 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: -0.53 (0.25), residues: 1029 helix: 0.67 (0.21), residues: 580 sheet: -0.61 (0.80), residues: 42 loop : -1.83 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 119 TYR 0.017 0.001 TYR F 88 PHE 0.017 0.002 PHE H 68 TRP 0.004 0.001 TRP K 86 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (14005) covalent geometry : angle 0.67787 / 0.38 (20007) hydrogen bonds : bond 0.04614 / 3.24 ( 722) hydrogen bonds : angle 3.86923 / 2.63 ( 1821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.76 seconds wall clock time: 42 minutes 57.42 seconds (2577.42 seconds total)