Starting phenix.real_space_refine on Thu Mar 5 13:36:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9f_31030/03_2026/7e9f_31030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9f_31030/03_2026/7e9f_31030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e9f_31030/03_2026/7e9f_31030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9f_31030/03_2026/7e9f_31030.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9f_31030/03_2026/7e9f_31030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9f_31030/03_2026/7e9f_31030.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12591 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 249 5.49 5 S 4 5.16 5 C 7588 2.51 5 N 2468 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.47, 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: 1.21 Conformation dependent library (CDL) restraints added in 240.8 milliseconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 55.5% alpha, 8.7% beta 117 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.609A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.596A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.745A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.623A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.530A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.308A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.526A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'D' and resid 40 through 49 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.542A pdb=" N LYS D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 107 through 127 removed outlier: 3.872A pdb=" N LYS D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.871A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.335A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.595A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.336A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.617A pdb=" N ASN G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.580A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 86 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.552A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 126 removed outlier: 3.574A pdb=" N LYS H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 30 Processing helix chain 'K' and resid 189 through 199 removed outlier: 4.403A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 212 removed outlier: 3.596A pdb=" N ALA K 204 " --> pdb=" O GLU K 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR K 212 " --> pdb=" O LEU K 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 189 through 199 removed outlier: 4.402A pdb=" N ALA L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 212 removed outlier: 3.597A pdb=" N ALA L 204 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU L 206 " --> pdb=" O ARG L 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR L 212 " --> pdb=" O LEU L 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.577A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.557A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.388A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.018A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain 'K' and resid 146 through 149 removed outlier: 5.857A pdb=" N PHE K 146 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS K 59 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG K 148 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL K 68 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 85 " --> pdb=" O ALA K 139 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA K 139 " --> pdb=" O LEU K 85 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA K 87 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU K 137 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR K 89 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR K 133 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG K 174 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU K 134 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE K 176 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALA K 136 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'L' and resid 146 through 149 removed outlier: 5.857A pdb=" N PHE L 146 " --> pdb=" O HIS L 59 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS L 59 " --> pdb=" O PHE L 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG L 148 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL L 68 " --> pdb=" O TYR L 90 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP L 86 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU L 74 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU L 85 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA L 139 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA L 87 " --> pdb=" O GLU L 137 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU L 137 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR L 89 " --> pdb=" O THR L 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR L 133 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG L 174 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU L 134 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE L 176 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ALA L 136 " --> pdb=" O ILE L 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.60 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=" C PHE G 26 " pdb=" N PRO G 27 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.86e+00 bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.80e+00 bond pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.20e+00 bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.05e+00 bond pdb=" C ACE K 1 " pdb=" O ACE K 1 " ideal model delta sigma weight residual 1.199 1.228 -0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 14000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 19382 1.91 - 3.82: 569 3.82 - 5.73: 37 5.73 - 7.64: 13 7.64 - 9.55: 6 Bond angle restraints: 20007 Sorted by residual: angle pdb=" C LYS L 28 " pdb=" N ARG L 29 " pdb=" CA ARG L 29 " ideal model delta sigma weight residual 121.54 128.73 -7.19 1.91e+00 2.74e-01 1.42e+01 angle pdb=" C LYS K 28 " pdb=" N ARG K 29 " pdb=" CA ARG K 29 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C TRP K 93 " pdb=" N PHE K 94 " pdb=" CA PHE K 94 " ideal model delta sigma weight residual 121.70 127.84 -6.14 1.80e+00 3.09e-01 1.16e+01 angle pdb=" C TRP L 93 " pdb=" N PHE L 94 " pdb=" CA PHE L 94 " ideal model delta sigma weight residual 121.70 127.81 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sigma weight residual 120.20 124.49 -4.29 1.50e+00 4.44e-01 8.20e+00 ... (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 - 0.038: 1566 0.038 - 0.077: 523 0.077 - 0.115: 181 0.115 - 0.153: 38 0.153 - 0.191: 8 Chirality restraints: 2316 Sorted by residual: 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=" 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 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.12e-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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.900 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.004 0.059 14005 Z= 0.182 Angle : 0.739 9.548 20007 Z= 0.436 Chirality : 0.044 0.191 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 covalent geometry : bond 0.00372 (14005) covalent geometry : angle 0.73907 (20007) hydrogen bonds : bond 0.13623 ( 722) hydrogen bonds : angle 5.82274 ( 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 : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8660 (mt) cc_final: 0.7930 (mp) REVERT: A 79 LYS cc_start: 0.8434 (tptm) cc_final: 0.8182 (tptp) REVERT: A 92 LEU cc_start: 0.9163 (mt) cc_final: 0.8861 (tp) REVERT: B 25 ASN cc_start: 0.8257 (m-40) cc_final: 0.8037 (m110) REVERT: B 35 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8008 (ttm110) REVERT: B 37 LEU cc_start: 0.9502 (mt) cc_final: 0.9119 (mt) REVERT: B 52 GLU cc_start: 0.8229 (tp30) cc_final: 0.7969 (tp30) REVERT: B 77 LYS cc_start: 0.8849 (mttt) cc_final: 0.8512 (mttm) REVERT: C 26 PHE cc_start: 0.8908 (m-80) cc_final: 0.8344 (m-10) REVERT: C 43 ARG cc_start: 0.8717 (mtp180) cc_final: 0.8452 (mtp-110) REVERT: C 53 THR cc_start: 0.8791 (m) cc_final: 0.8570 (m) REVERT: C 96 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8555 (ttmt) REVERT: D 46 LYS cc_start: 0.9348 (ttmt) cc_final: 0.9125 (ttmm) REVERT: D 79 GLU cc_start: 0.8327 (tp30) cc_final: 0.7725 (tp30) REVERT: E 54 PHE cc_start: 0.7397 (m-80) cc_final: 0.6547 (m-10) REVERT: E 69 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7828 (ptp90) REVERT: F 40 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7776 (ttt180) REVERT: F 83 SER cc_start: 0.8232 (p) cc_final: 0.8021 (m) REVERT: G 39 ASN cc_start: 0.8404 (m-40) cc_final: 0.8088 (p0) REVERT: H 43 TYR cc_start: 0.7620 (m-80) cc_final: 0.7174 (m-80) REVERT: H 46 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9120 (ttmm) REVERT: H 86 TYR cc_start: 0.7918 (m-10) cc_final: 0.7561 (m-10) REVERT: K 49 LYS cc_start: 0.6236 (mtmt) cc_final: 0.5394 (mmtp) REVERT: L 49 LYS cc_start: 0.6371 (mtmt) cc_final: 0.5668 (mmtp) REVERT: L 79 LEU cc_start: 0.7380 (mt) cc_final: 0.6588 (mp) REVERT: L 134 LEU cc_start: 0.7157 (mt) cc_final: 0.6932 (tt) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.1727 time to fit residues: 84.5631 Evaluate side-chains 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** 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 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 ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 ASN L 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.118250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084746 restraints weight = 40783.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086850 restraints weight = 24173.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.088157 restraints weight = 17876.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089027 restraints weight = 15254.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089187 restraints weight = 13988.153| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14005 Z= 0.197 Angle : 0.654 9.118 20007 Z= 0.368 Chirality : 0.039 0.160 2316 Planarity : 0.005 0.053 1668 Dihedral : 31.444 147.389 3864 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.56 % Allowed : 20.31 % Favored : 74.12 % 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: -2.27 (0.23), residues: 1029 helix: -0.70 (0.19), residues: 574 sheet: -2.54 (0.65), residues: 40 loop : -2.52 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 95 TYR 0.017 0.002 TYR K 40 PHE 0.009 0.002 PHE A 104 TRP 0.009 0.001 TRP L 86 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00440 (14005) covalent geometry : angle 0.65376 (20007) hydrogen bonds : bond 0.04757 ( 722) hydrogen bonds : angle 4.04850 ( 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 319 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.401 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: 0.7944 (mttt) cc_final: 0.7666 (mttm) REVERT: B 35 ARG cc_start: 0.8550 (mtp-110) cc_final: 0.8046 (ttm110) REVERT: B 40 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8301 (mmm-85) REVERT: B 90 LEU cc_start: 0.9358 (mt) cc_final: 0.8995 (mt) REVERT: C 43 ARG cc_start: 0.8696 (mtp180) cc_final: 0.8405 (mtp-110) REVERT: C 100 ASN cc_start: 0.8056 (p0) cc_final: 0.7804 (p0) REVERT: E 51 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8354 (tt) REVERT: E 54 PHE cc_start: 0.7551 (m-80) cc_final: 0.6891 (m-10) REVERT: E 59 GLU cc_start: 0.8626 (pm20) cc_final: 0.8179 (pm20) REVERT: E 69 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8074 (ptp90) REVERT: E 129 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7450 (ttp80) REVERT: F 52 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7524 (tp30) REVERT: F 83 SER cc_start: 0.8802 (p) cc_final: 0.8377 (t) REVERT: H 86 TYR cc_start: 0.8198 (m-10) cc_final: 0.7609 (m-10) REVERT: K 49 LYS cc_start: 0.6270 (mtmt) cc_final: 0.5483 (mmtp) REVERT: K 79 LEU cc_start: 0.7247 (mt) cc_final: 0.6630 (mp) REVERT: L 49 LYS cc_start: 0.6559 (mtmt) cc_final: 0.5884 (mmtp) REVERT: L 79 LEU cc_start: 0.7186 (mt) cc_final: 0.6926 (mt) REVERT: L 148 ARG cc_start: 0.6275 (ptt-90) cc_final: 0.5793 (pmt170) outliers start: 46 outliers final: 31 residues processed: 301 average time/residue: 0.1624 time to fit residues: 63.9437 Evaluate side-chains 262 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 86 SER 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 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 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 H residue 101 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 L residue 57 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 30.0000 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.117598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083911 restraints weight = 41193.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085882 restraints weight = 25005.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087175 restraints weight = 18828.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087910 restraints weight = 16178.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088219 restraints weight = 14966.503| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14005 Z= 0.172 Angle : 0.620 8.078 20007 Z= 0.352 Chirality : 0.038 0.170 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.301 147.773 3864 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.29 % Allowed : 21.77 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1029 helix: 0.18 (0.21), residues: 577 sheet: -1.99 (0.72), residues: 40 loop : -2.30 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.013 0.001 TYR L 40 PHE 0.012 0.002 PHE G 26 TRP 0.009 0.001 TRP L 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00387 (14005) covalent geometry : angle 0.61966 (20007) hydrogen bonds : bond 0.04472 ( 722) hydrogen bonds : angle 3.86790 ( 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 304 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 0.362 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: symmetry clash REVERT: A 76 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: A 97 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 25 ASN cc_start: 0.8516 (m-40) cc_final: 0.8058 (m110) REVERT: B 35 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.8036 (ttm-80) REVERT: B 90 LEU cc_start: 0.9382 (mt) cc_final: 0.9121 (mt) REVERT: C 100 ASN cc_start: 0.8006 (p0) cc_final: 0.7560 (p0) REVERT: D 79 GLU cc_start: 0.7907 (tp30) cc_final: 0.7688 (tp30) REVERT: D 86 TYR cc_start: 0.8120 (m-10) cc_final: 0.7588 (m-10) REVERT: E 54 PHE cc_start: 0.7465 (m-80) cc_final: 0.7061 (m-10) REVERT: E 59 GLU cc_start: 0.8572 (pm20) cc_final: 0.8293 (pm20) REVERT: E 69 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8233 (mtp180) REVERT: E 73 GLU cc_start: 0.7926 (tt0) cc_final: 0.7561 (tt0) REVERT: F 52 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7574 (tp30) REVERT: F 83 SER cc_start: 0.8739 (p) cc_final: 0.8273 (t) REVERT: G 59 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8514 (tp) REVERT: H 95 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7884 (mtp85) REVERT: K 73 GLU cc_start: 0.7240 (mp0) cc_final: 0.6855 (pt0) REVERT: K 148 ARG cc_start: 0.6653 (ptt-90) cc_final: 0.6231 (ptt90) REVERT: L 49 LYS cc_start: 0.6465 (mtmt) cc_final: 0.5823 (mmtp) REVERT: L 148 ARG cc_start: 0.6171 (ptt-90) cc_final: 0.5789 (pmt170) REVERT: L 193 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8620 (mmmt) outliers start: 52 outliers final: 37 residues processed: 286 average time/residue: 0.1626 time to fit residues: 60.6132 Evaluate side-chains 266 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 76 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 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 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 124 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 119 optimal weight: 30.0000 chunk 112 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.113751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079847 restraints weight = 41079.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081734 restraints weight = 25090.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082966 restraints weight = 18913.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083637 restraints weight = 16327.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083931 restraints weight = 15184.376| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14005 Z= 0.292 Angle : 0.738 10.574 20007 Z= 0.407 Chirality : 0.043 0.172 2316 Planarity : 0.005 0.050 1668 Dihedral : 31.377 148.898 3864 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 7.26 % Allowed : 24.91 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1029 helix: 0.14 (0.21), residues: 581 sheet: -2.14 (0.71), residues: 40 loop : -2.22 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 35 TYR 0.050 0.002 TYR F 88 PHE 0.019 0.002 PHE G 26 TRP 0.004 0.001 TRP L 86 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00660 (14005) covalent geometry : angle 0.73830 (20007) hydrogen bonds : bond 0.05857 ( 722) hydrogen bonds : angle 4.29088 ( 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 284 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8327 (ttm-80) REVERT: B 46 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8574 (mm) REVERT: C 100 ASN cc_start: 0.7969 (p0) cc_final: 0.7720 (p0) REVERT: D 79 GLU cc_start: 0.8123 (tp30) cc_final: 0.7551 (tp30) REVERT: D 116 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8152 (tm-30) REVERT: E 54 PHE cc_start: 0.7452 (m-80) cc_final: 0.6823 (m-10) REVERT: E 59 GLU cc_start: 0.8656 (pm20) cc_final: 0.7980 (pm20) REVERT: E 64 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7581 (mttp) REVERT: E 69 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8342 (mtp180) REVERT: E 123 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8084 (t0) REVERT: E 129 ARG cc_start: 0.8193 (tpt-90) cc_final: 0.7951 (tpp80) REVERT: F 52 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7845 (tp30) REVERT: F 83 SER cc_start: 0.8733 (p) cc_final: 0.8132 (t) REVERT: F 84 LEU cc_start: 0.9241 (tp) cc_final: 0.9024 (tp) REVERT: H 75 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7689 (ttm170) REVERT: L 48 ILE cc_start: 0.6164 (mm) cc_final: 0.5840 (mp) REVERT: L 49 LYS cc_start: 0.6702 (mtmt) cc_final: 0.5964 (mmtp) REVERT: L 193 LYS cc_start: 0.8937 (mtpp) cc_final: 0.8621 (mmmt) outliers start: 60 outliers final: 44 residues processed: 265 average time/residue: 0.1525 time to fit residues: 53.7946 Evaluate side-chains 249 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 LEU 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 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 72 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 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 65 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.117710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084460 restraints weight = 40993.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086474 restraints weight = 24294.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087798 restraints weight = 18144.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088400 restraints weight = 15570.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.088879 restraints weight = 14490.811| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14005 Z= 0.154 Angle : 0.625 8.666 20007 Z= 0.354 Chirality : 0.038 0.172 2316 Planarity : 0.004 0.047 1668 Dihedral : 31.116 148.235 3864 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.99 % Allowed : 28.42 % Favored : 67.59 % 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: -0.78 (0.25), residues: 1029 helix: 0.60 (0.21), residues: 580 sheet: -1.65 (0.72), residues: 42 loop : -2.06 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.026 0.002 TYR F 88 PHE 0.011 0.001 PHE A 84 TRP 0.007 0.001 TRP L 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00345 (14005) covalent geometry : angle 0.62451 (20007) hydrogen bonds : bond 0.04377 ( 722) hydrogen bonds : angle 3.80125 ( 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 281 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8399 (m-40) cc_final: 0.8063 (m110) REVERT: B 72 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7184 (t80) REVERT: C 26 PHE cc_start: 0.9058 (m-80) cc_final: 0.8746 (m-10) REVERT: C 100 ASN cc_start: 0.8055 (p0) cc_final: 0.7765 (p0) REVERT: D 86 TYR cc_start: 0.8205 (m-10) cc_final: 0.7144 (m-10) REVERT: E 69 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8154 (mtp180) REVERT: F 25 ASN cc_start: 0.8253 (m110) cc_final: 0.7988 (m110) REVERT: F 52 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7455 (tp30) REVERT: F 75 HIS cc_start: 0.9194 (OUTLIER) cc_final: 0.8519 (t70) REVERT: F 83 SER cc_start: 0.8395 (p) cc_final: 0.7847 (t) REVERT: F 84 LEU cc_start: 0.8959 (tp) cc_final: 0.8090 (tp) REVERT: F 88 TYR cc_start: 0.8289 (m-10) cc_final: 0.8035 (m-80) REVERT: G 30 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7666 (ttm-80) REVERT: L 48 ILE cc_start: 0.6288 (mm) cc_final: 0.5974 (mp) REVERT: L 49 LYS cc_start: 0.6728 (mtmt) cc_final: 0.6008 (mmtp) REVERT: L 73 GLU cc_start: 0.7372 (mp0) cc_final: 0.6628 (mt-10) REVERT: L 193 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8574 (mmmt) outliers start: 33 outliers final: 23 residues processed: 270 average time/residue: 0.1593 time to fit residues: 56.4496 Evaluate side-chains 244 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain B residue 72 TYR 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 C residue 77 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 50 ILE Chi-restraints excluded: chain F residue 75 HIS 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 K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 40.0000 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 HIS K 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.115650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.082054 restraints weight = 41069.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.084009 restraints weight = 24754.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085241 restraints weight = 18693.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085909 restraints weight = 16152.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086193 restraints weight = 15026.501| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14005 Z= 0.203 Angle : 0.666 8.416 20007 Z= 0.372 Chirality : 0.040 0.174 2316 Planarity : 0.004 0.047 1668 Dihedral : 31.151 148.627 3864 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.17 % Allowed : 28.17 % 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: -0.84 (0.25), residues: 1029 helix: 0.50 (0.21), residues: 581 sheet: -1.80 (0.72), residues: 42 loop : -1.99 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 35 TYR 0.026 0.002 TYR F 88 PHE 0.014 0.002 PHE G 26 TRP 0.015 0.002 TRP L 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00462 (14005) covalent geometry : angle 0.66614 (20007) hydrogen bonds : bond 0.04779 ( 722) hydrogen bonds : angle 3.93357 ( 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: 51 poor density : 228 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: B 25 ASN cc_start: 0.8433 (m-40) cc_final: 0.8185 (m-40) REVERT: B 46 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8777 (mt) REVERT: C 26 PHE cc_start: 0.9197 (m-80) cc_final: 0.8965 (m-80) REVERT: C 100 ASN cc_start: 0.8105 (p0) cc_final: 0.7740 (p0) REVERT: D 79 GLU cc_start: 0.7844 (tp30) cc_final: 0.7430 (tp30) REVERT: D 86 TYR cc_start: 0.8249 (m-10) cc_final: 0.7616 (m-10) REVERT: D 116 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8043 (tm-30) REVERT: E 69 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8155 (mtp180) REVERT: E 70 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8089 (tp) REVERT: E 105 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: F 25 ASN cc_start: 0.8267 (m110) cc_final: 0.8031 (m110) REVERT: F 52 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7669 (tp30) REVERT: F 75 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8302 (t70) REVERT: F 83 SER cc_start: 0.8469 (p) cc_final: 0.7934 (t) REVERT: F 84 LEU cc_start: 0.8979 (tp) cc_final: 0.8492 (tp) REVERT: F 88 TYR cc_start: 0.8321 (m-10) cc_final: 0.8043 (m-80) REVERT: G 30 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7766 (ttm-80) REVERT: K 48 ILE cc_start: 0.6165 (mm) cc_final: 0.5908 (mp) REVERT: K 49 LYS cc_start: 0.6282 (ptmt) cc_final: 0.5714 (mmtp) REVERT: K 133 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.4620 (m-80) REVERT: L 49 LYS cc_start: 0.6615 (mtmt) cc_final: 0.5887 (mmtp) REVERT: L 133 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: L 193 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8621 (mmmt) outliers start: 51 outliers final: 33 residues processed: 258 average time/residue: 0.1386 time to fit residues: 48.8337 Evaluate side-chains 243 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 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 29 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 VAL 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 C residue 77 THR 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 70 LEU 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 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain 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 59 HIS Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 0.9990 chunk 105 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.117390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084164 restraints weight = 40927.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.086225 restraints weight = 24020.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.087511 restraints weight = 17900.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.088221 restraints weight = 15385.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088514 restraints weight = 14261.330| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14005 Z= 0.160 Angle : 0.641 8.797 20007 Z= 0.361 Chirality : 0.039 0.197 2316 Planarity : 0.004 0.046 1668 Dihedral : 31.071 148.347 3864 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.20 % Allowed : 29.38 % Favored : 65.42 % 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: -0.75 (0.25), residues: 1029 helix: 0.65 (0.21), residues: 581 sheet: -1.58 (0.55), residues: 70 loop : -2.09 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 35 TYR 0.026 0.002 TYR H 43 PHE 0.013 0.001 PHE D 68 TRP 0.014 0.001 TRP L 86 HIS 0.011 0.001 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00359 (14005) covalent geometry : angle 0.64118 (20007) hydrogen bonds : bond 0.04356 ( 722) hydrogen bonds : angle 3.82141 ( 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 272 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.408 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: B 72 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 100 ASN cc_start: 0.8009 (p0) cc_final: 0.7674 (p0) REVERT: D 86 TYR cc_start: 0.8160 (m-10) cc_final: 0.7109 (m-10) REVERT: E 69 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8056 (mtp180) REVERT: E 70 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8048 (tp) REVERT: F 25 ASN cc_start: 0.8281 (m110) cc_final: 0.7989 (m110) REVERT: F 52 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7467 (tp30) REVERT: F 75 HIS cc_start: 0.9119 (OUTLIER) cc_final: 0.8420 (t70) REVERT: F 83 SER cc_start: 0.8447 (p) cc_final: 0.7939 (t) REVERT: F 84 LEU cc_start: 0.9000 (tp) cc_final: 0.8347 (tp) REVERT: F 88 TYR cc_start: 0.8243 (m-10) cc_final: 0.7957 (m-80) REVERT: G 30 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: H 43 TYR cc_start: 0.7696 (m-80) cc_final: 0.7290 (m-80) REVERT: K 48 ILE cc_start: 0.6423 (mm) cc_final: 0.6116 (mp) REVERT: K 133 TYR cc_start: 0.5428 (OUTLIER) cc_final: 0.4718 (m-80) REVERT: L 48 ILE cc_start: 0.6189 (mm) cc_final: 0.5902 (mt) REVERT: L 49 LYS cc_start: 0.6594 (mtmt) cc_final: 0.5878 (mmtp) REVERT: L 193 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8627 (mmmt) outliers start: 43 outliers final: 34 residues processed: 256 average time/residue: 0.1406 time to fit residues: 48.9086 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 : 0.355 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 TYR 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 C residue 77 THR Chi-restraints excluded: chain D residue 39 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 86 SER 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 65 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 25 THR 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 133 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4022 r_free = 0.4022 target = 0.115406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082101 restraints weight = 40753.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083923 restraints weight = 25428.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.085095 restraints weight = 19396.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085752 restraints weight = 16789.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.085885 restraints weight = 15612.819| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14005 Z= 0.220 Angle : 0.687 9.289 20007 Z= 0.382 Chirality : 0.040 0.174 2316 Planarity : 0.005 0.066 1668 Dihedral : 31.156 148.681 3864 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.65 % Allowed : 28.66 % Favored : 64.69 % 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: -0.94 (0.25), residues: 1029 helix: 0.52 (0.21), residues: 581 sheet: -2.24 (0.59), residues: 54 loop : -2.14 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 35 TYR 0.025 0.002 TYR H 43 PHE 0.015 0.002 PHE D 73 TRP 0.012 0.001 TRP L 86 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00501 (14005) covalent geometry : angle 0.68703 (20007) hydrogen bonds : bond 0.04962 ( 722) hydrogen bonds : angle 3.98566 ( 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 273 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 0.225 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: B 26 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8644 (tp) REVERT: B 72 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7280 (t80) REVERT: C 26 PHE cc_start: 0.8678 (m-80) cc_final: 0.8415 (m-10) REVERT: C 100 ASN cc_start: 0.8042 (p0) cc_final: 0.7709 (p0) REVERT: D 79 GLU cc_start: 0.7874 (tp30) cc_final: 0.7487 (tp30) REVERT: D 86 TYR cc_start: 0.8242 (m-10) cc_final: 0.7186 (m-10) REVERT: E 69 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8143 (mtp180) REVERT: E 70 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8081 (tp) REVERT: E 105 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: F 25 ASN cc_start: 0.8312 (m110) cc_final: 0.8000 (m110) REVERT: F 52 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7630 (tp30) REVERT: F 75 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8881 (t70) REVERT: F 83 SER cc_start: 0.8468 (p) cc_final: 0.7947 (t) REVERT: G 30 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7799 (ttm-80) REVERT: G 65 GLU cc_start: 0.8373 (pp20) cc_final: 0.7942 (pp20) REVERT: K 48 ILE cc_start: 0.6773 (mm) cc_final: 0.6464 (mp) REVERT: K 133 TYR cc_start: 0.5351 (OUTLIER) cc_final: 0.4689 (m-80) REVERT: L 48 ILE cc_start: 0.6057 (mm) cc_final: 0.5779 (mt) REVERT: L 49 LYS cc_start: 0.6602 (mtmt) cc_final: 0.5895 (mmtp) REVERT: L 133 TYR cc_start: 0.5694 (OUTLIER) cc_final: 0.5029 (m-80) REVERT: L 193 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8591 (mmmt) outliers start: 55 outliers final: 41 residues processed: 259 average time/residue: 0.1308 time to fit residues: 46.4752 Evaluate side-chains 252 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 TYR 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 77 THR Chi-restraints excluded: chain D residue 39 THR 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 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 25 THR 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 133 TYR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.116749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.083811 restraints weight = 41003.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085680 restraints weight = 25045.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086899 restraints weight = 18977.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087593 restraints weight = 16406.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.087894 restraints weight = 15223.574| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14005 Z= 0.178 Angle : 0.665 9.137 20007 Z= 0.372 Chirality : 0.039 0.218 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.067 148.518 3864 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.56 % Allowed : 30.71 % Favored : 63.72 % 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: -0.73 (0.25), residues: 1029 helix: 0.62 (0.21), residues: 579 sheet: -1.51 (0.57), residues: 70 loop : -2.02 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 35 TYR 0.033 0.001 TYR F 88 PHE 0.017 0.002 PHE G 26 TRP 0.013 0.001 TRP L 86 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00406 (14005) covalent geometry : angle 0.66538 (20007) hydrogen bonds : bond 0.04490 ( 722) hydrogen bonds : angle 3.86490 ( 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 260 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7826 (ttp-170) REVERT: B 72 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7289 (t80) REVERT: C 26 PHE cc_start: 0.8666 (m-80) cc_final: 0.8410 (m-10) REVERT: D 86 TYR cc_start: 0.8182 (m-10) cc_final: 0.7191 (m-10) REVERT: E 69 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8071 (mtp180) REVERT: E 70 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8031 (tp) REVERT: E 105 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: F 25 ASN cc_start: 0.8294 (m110) cc_final: 0.7989 (m110) REVERT: F 52 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7430 (tp30) REVERT: F 75 HIS cc_start: 0.9193 (OUTLIER) cc_final: 0.8840 (t70) REVERT: F 83 SER cc_start: 0.8471 (p) cc_final: 0.8033 (t) REVERT: H 43 TYR cc_start: 0.7941 (m-80) cc_final: 0.7514 (m-80) REVERT: K 48 ILE cc_start: 0.6797 (mm) cc_final: 0.6509 (mp) REVERT: K 133 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.4840 (m-80) REVERT: L 48 ILE cc_start: 0.6062 (mm) cc_final: 0.5762 (mt) REVERT: L 49 LYS cc_start: 0.6616 (mtmt) cc_final: 0.5906 (mmtp) REVERT: L 133 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.5130 (m-80) REVERT: L 193 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8598 (mmmt) outliers start: 46 outliers final: 37 residues processed: 248 average time/residue: 0.1370 time to fit residues: 46.4776 Evaluate side-chains 250 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 HIS 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 65 VAL Chi-restraints excluded: chain B residue 72 TYR 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 C residue 77 THR 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 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 65 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 25 THR 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 133 TYR 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 133 TYR Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.118891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.085892 restraints weight = 41262.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087877 restraints weight = 24668.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.089158 restraints weight = 18530.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089747 restraints weight = 15972.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090255 restraints weight = 14882.478| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14005 Z= 0.151 Angle : 0.654 9.511 20007 Z= 0.366 Chirality : 0.039 0.209 2316 Planarity : 0.004 0.054 1668 Dihedral : 30.897 148.279 3864 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.72 % Allowed : 32.04 % Favored : 63.24 % 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 (0.26), residues: 1029 helix: 0.86 (0.22), residues: 575 sheet: -1.50 (0.55), residues: 70 loop : -2.02 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 35 TYR 0.015 0.001 TYR D 43 PHE 0.019 0.001 PHE D 68 TRP 0.014 0.001 TRP L 86 HIS 0.004 0.001 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00338 (14005) covalent geometry : angle 0.65383 (20007) hydrogen bonds : bond 0.04329 ( 722) hydrogen bonds : angle 3.73860 ( 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 266 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7812 (ttp-170) REVERT: B 72 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7338 (t80) REVERT: C 43 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.7860 (mtp85) REVERT: C 72 ARG cc_start: 0.7430 (mmp80) cc_final: 0.7212 (mmp80) REVERT: C 82 ARG cc_start: 0.8430 (tpt-90) cc_final: 0.8191 (tpt-90) REVERT: D 86 TYR cc_start: 0.7993 (m-10) cc_final: 0.7108 (m-10) REVERT: E 69 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8005 (mtp180) REVERT: E 70 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7911 (tp) REVERT: F 25 ASN cc_start: 0.8187 (m110) cc_final: 0.7963 (m110) REVERT: F 75 HIS cc_start: 0.9114 (OUTLIER) cc_final: 0.8023 (t70) REVERT: F 83 SER cc_start: 0.8344 (p) cc_final: 0.8005 (t) REVERT: G 65 GLU cc_start: 0.8185 (pp20) cc_final: 0.7856 (pp20) REVERT: G 82 ARG cc_start: 0.8730 (tpt90) cc_final: 0.8315 (tpt90) REVERT: K 48 ILE cc_start: 0.6825 (mm) cc_final: 0.6515 (mp) REVERT: K 133 TYR cc_start: 0.5651 (OUTLIER) cc_final: 0.4924 (m-80) REVERT: L 48 ILE cc_start: 0.6222 (mm) cc_final: 0.5985 (mt) REVERT: L 49 LYS cc_start: 0.6635 (mtmt) cc_final: 0.5955 (mmtp) REVERT: L 133 TYR cc_start: 0.5388 (OUTLIER) cc_final: 0.4694 (m-80) REVERT: L 193 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8614 (mmmt) outliers start: 39 outliers final: 30 residues processed: 253 average time/residue: 0.1535 time to fit residues: 51.2993 Evaluate side-chains 247 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain A residue 113 HIS 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 72 TYR 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 C residue 77 THR 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 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER 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 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 133 TYR 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 133 TYR Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.119017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086155 restraints weight = 40827.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088133 restraints weight = 24476.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089424 restraints weight = 18368.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090124 restraints weight = 15841.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.090408 restraints weight = 14688.586| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14005 Z= 0.154 Angle : 0.657 9.501 20007 Z= 0.366 Chirality : 0.039 0.200 2316 Planarity : 0.004 0.052 1668 Dihedral : 30.866 147.912 3864 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.35 % Allowed : 33.25 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1029 helix: 0.84 (0.22), residues: 577 sheet: -1.96 (0.60), residues: 54 loop : -1.97 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 35 TYR 0.018 0.001 TYR F 88 PHE 0.019 0.002 PHE D 68 TRP 0.010 0.001 TRP K 86 HIS 0.002 0.001 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00347 (14005) covalent geometry : angle 0.65690 (20007) hydrogen bonds : bond 0.04382 ( 722) hydrogen bonds : angle 3.71644 ( 1821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2484.32 seconds wall clock time: 43 minutes 19.49 seconds (2599.49 seconds total)