Starting phenix.real_space_refine on Sun Sep 13 09:20:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1k_0590/09_2026/6o1k_0590_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1k_0590/09_2026/6o1k_0590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o1k_0590/09_2026/6o1k_0590_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1k_0590/09_2026/6o1k_0590_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o1k_0590/09_2026/6o1k_0590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1k_0590/09_2026/6o1k_0590.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 S 30 5.16 5 C 7194 2.51 5 N 2033 2.21 5 O 2139 1.98 5 H 11277 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22707 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "D" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "E" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "F" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "G" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "H" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "I" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "J" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "K" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "L" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1095 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain: "M" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "N" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "O" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Classifications: {'RNA': 18} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 17} Chain: "P" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Classifications: {'RNA': 18} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 17} Time building chain proxies: 4.29, per 1000 atoms: 0.19 Number of scatterers: 22707 At special positions: 0 Unit cell: (97.01, 123.17, 79.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 34 15.00 O 2139 8.00 N 2033 7.00 C 7194 6.00 H 11277 1.00 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: 2.11 Conformation dependent library (CDL) restraints added in 588.1 milliseconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 22.5% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.612A pdb=" N GLN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.708A pdb=" N ASP A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.602A pdb=" N GLN B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.751A pdb=" N ASP B 45 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.710A pdb=" N GLU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.897A pdb=" N ARG B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.678A pdb=" N GLU C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 18 removed outlier: 3.694A pdb=" N TYR D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 18 removed outlier: 3.783A pdb=" N TYR E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.565A pdb=" N TYR G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 18 removed outlier: 3.503A pdb=" N THR H 14 " --> pdb=" O PRO H 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 18 removed outlier: 3.551A pdb=" N TYR I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU I 18 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 18 removed outlier: 3.920A pdb=" N GLU J 18 " --> pdb=" O THR J 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 19 removed outlier: 3.639A pdb=" N THR K 14 " --> pdb=" O PRO K 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 18 removed outlier: 3.504A pdb=" N TYR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU L 12 " --> pdb=" O GLN L 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 18 removed outlier: 3.793A pdb=" N TYR M 11 " --> pdb=" O LEU M 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 17 removed outlier: 3.574A pdb=" N TYR N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 6.877A pdb=" N ARG A 2 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N CYS A 32 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 4 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLN A 34 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A 6 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.846A pdb=" N SER A 103 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS A 146 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 105 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N SER A 148 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 107 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.804A pdb=" N ARG B 2 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N CYS B 32 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 4 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN B 34 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 250 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA B 235 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 252 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81 Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 64 removed outlier: 7.283A pdb=" N LEU C 45 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N PHE C 39 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER D 60 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 61 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE D 36 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS D 47 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER D 38 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER E 60 " --> pdb=" O TYR D 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.663A pdb=" N SER F 60 " --> pdb=" O TYR E 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 39 removed outlier: 6.492A pdb=" N LEU F 45 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE F 39 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER F 51 " --> pdb=" O PRO H 64 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER H 60 " --> pdb=" O TYR F 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 31 through 34 removed outlier: 6.681A pdb=" N SER G 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET H 53 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER H 51 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL H 43 " --> pdb=" O PHE H 39 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE H 39 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU H 45 " --> pdb=" O GLU H 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.991A pdb=" N SER G 38 " --> pdb=" O LEU G 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 31 through 34 removed outlier: 6.883A pdb=" N SER I 60 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL N 43 " --> pdb=" O PHE N 39 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE N 39 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU N 45 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER N 60 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET M 53 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER M 51 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL M 43 " --> pdb=" O PHE M 39 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE M 39 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU M 45 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 43 through 46 removed outlier: 6.898A pdb=" N SER J 60 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN J 35 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU J 45 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE J 39 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER J 51 " --> pdb=" O PRO K 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER K 60 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU K 45 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE K 39 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL K 43 " --> pdb=" O PHE K 39 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER K 51 " --> pdb=" O PRO L 64 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER L 60 " --> pdb=" O TYR K 55 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR L 25 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL L 62 " --> pdb=" O SER L 23 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER L 23 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN L 35 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU L 45 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE L 39 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL L 43 " --> pdb=" O PHE L 39 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER L 51 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER M 60 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.08: 3269 1.08 - 1.26: 9715 1.26 - 1.45: 3405 1.45 - 1.63: 6597 1.63 - 1.81: 52 Bond restraints: 23038 Sorted by residual: bond pdb=" C2 A P 3 " pdb=" H2 A P 3 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 PHE B 41 " pdb=" HD2 PHE B 41 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C8 A P 16 " pdb=" H8 A P 16 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN K 48 " pdb="HD21 ASN K 48 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ2 TRP B 203 " pdb=" HZ2 TRP B 203 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 23033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 41359 5.96 - 11.93: 304 11.93 - 17.89: 17 17.89 - 23.85: 2 23.85 - 29.82: 2 Bond angle restraints: 41684 Sorted by residual: angle pdb=" C6 A O 14 " pdb=" N6 A O 14 " pdb=" H61 A O 14 " ideal model delta sigma weight residual 120.00 90.18 29.82 3.00e+00 1.11e-01 9.88e+01 angle pdb=" C6 A O 11 " pdb=" N6 A O 11 " pdb=" H61 A O 11 " ideal model delta sigma weight residual 120.00 149.33 -29.33 3.00e+00 1.11e-01 9.56e+01 angle pdb=" C ARG H 69 " pdb=" N LEU H 70 " pdb=" CA LEU H 70 " ideal model delta sigma weight residual 120.68 131.97 -11.29 1.52e+00 4.33e-01 5.52e+01 angle pdb=" C6 A P 2 " pdb=" N6 A P 2 " pdb=" H61 A P 2 " ideal model delta sigma weight residual 120.00 140.57 -20.57 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C6 A P 10 " pdb=" N6 A P 10 " pdb=" H61 A P 10 " ideal model delta sigma weight residual 120.00 100.62 19.38 3.00e+00 1.11e-01 4.18e+01 ... (remaining 41679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9750 17.64 - 35.28: 488 35.28 - 52.92: 205 52.92 - 70.57: 278 70.57 - 88.21: 35 Dihedral angle restraints: 10756 sinusoidal: 6214 harmonic: 4542 Sorted by residual: dihedral pdb=" CA VAL G 50 " pdb=" C VAL G 50 " pdb=" N SER G 51 " pdb=" CA SER G 51 " ideal model delta harmonic sigma weight residual -180.00 -129.61 -50.39 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ASP H 9 " pdb=" C ASP H 9 " pdb=" N PRO H 10 " pdb=" CA PRO H 10 " ideal model delta harmonic sigma weight residual 180.00 135.43 44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA GLN G 52 " pdb=" C GLN G 52 " pdb=" N MET G 53 " pdb=" CA MET G 53 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 10753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1367 0.066 - 0.131: 379 0.131 - 0.197: 75 0.197 - 0.263: 19 0.263 - 0.328: 5 Chirality restraints: 1845 Sorted by residual: chirality pdb=" CA ASP A 199 " pdb=" N ASP A 199 " pdb=" C ASP A 199 " pdb=" CB ASP A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB ILE N 24 " pdb=" CA ILE N 24 " pdb=" CG1 ILE N 24 " pdb=" CG2 ILE N 24 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PRO B 226 " pdb=" N PRO B 226 " pdb=" C PRO B 226 " pdb=" CB PRO B 226 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1842 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 255 " -0.216 2.00e-02 2.50e+03 9.37e-02 3.51e+02 pdb=" CG TRP B 255 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 255 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 255 " 0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP B 255 " 0.091 2.00e-02 2.50e+03 pdb=" CE2 TRP B 255 " 0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP B 255 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 255 " -0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 255 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B 255 " -0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP B 255 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 TRP B 255 " 0.151 2.00e-02 2.50e+03 pdb=" HE3 TRP B 255 " 0.125 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 255 " -0.101 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 255 " 0.033 2.00e-02 2.50e+03 pdb=" HH2 TRP B 255 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 A O 5 " 0.079 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" N6 A O 5 " -0.319 2.00e-02 2.50e+03 pdb=" H61 A O 5 " 0.119 2.00e-02 2.50e+03 pdb=" H62 A O 5 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 A O 1 " 0.074 2.00e-02 2.50e+03 1.68e-01 2.81e+02 pdb=" N6 A O 1 " -0.289 2.00e-02 2.50e+03 pdb=" H61 A O 1 " 0.107 2.00e-02 2.50e+03 pdb=" H62 A O 1 " 0.108 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 221 1.79 - 2.49: 14413 2.49 - 3.20: 69486 3.20 - 3.90: 95111 3.90 - 4.60: 145176 Nonbonded interactions: 324407 Sorted by model distance: nonbonded pdb=" HG SER E 38 " pdb=" H PHE E 39 " model vdw 1.091 2.100 nonbonded pdb=" HG SER J 60 " pdb=" H THR J 61 " model vdw 1.251 2.100 nonbonded pdb=" HG SER C 60 " pdb=" H THR C 61 " model vdw 1.270 2.100 nonbonded pdb=" HG SER M 60 " pdb=" H THR M 61 " model vdw 1.273 2.100 nonbonded pdb=" HD2 TYR K 55 " pdb=" HE2 HIS K 57 " model vdw 1.317 2.100 ... (remaining 324402 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 6 through 69) selection = (chain 'D' and resid 6 through 69) selection = (chain 'E' and resid 6 through 69) selection = (chain 'F' and resid 6 through 69) selection = (chain 'G' and resid 6 through 69) selection = (chain 'H' and resid 6 through 69) selection = (chain 'I' and resid 6 through 69) selection = (chain 'J' and resid 6 through 69) selection = (chain 'K' and resid 6 through 69) selection = (chain 'L' and resid 6 through 69) selection = (chain 'M' and resid 6 through 69) selection = (chain 'N' and resid 6 through 69) } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 26.880 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.006 0.049 11761 Z= 0.324 Angle : 1.070 12.333 16127 Z= 0.660 Chirality : 0.065 0.328 1845 Planarity : 0.011 0.182 1926 Dihedral : 12.092 81.045 4597 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -3.06 (0.21), residues: 1289 helix: -3.47 (0.19), residues: 251 sheet: -2.01 (0.21), residues: 464 loop : -1.08 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 229 TYR 0.065 0.004 TYR A 143 PHE 0.050 0.005 PHE A 243 TRP 0.132 0.015 TRP B 255 HIS 0.013 0.003 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.32 (11761) covalent geometry : angle 1.06992 / 0.66 (16127) hydrogen bonds : bond 0.17923 / 11.74 ( 409) hydrogen bonds : angle 8.30525 / 5.31 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 396 time to evaluate : 0.635 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: 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: symmetry clash REVERT: A 35 ASP cc_start: 0.7999 (p0) cc_final: 0.7528 (p0) REVERT: A 41 PHE cc_start: 0.7926 (t80) cc_final: 0.7709 (t80) REVERT: A 135 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7800 (tptp) REVERT: A 139 LYS cc_start: 0.8814 (mttt) cc_final: 0.8581 (mttm) REVERT: B 134 SER cc_start: 0.9138 (t) cc_final: 0.8911 (p) REVERT: B 135 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7845 (tptt) REVERT: B 211 GLU cc_start: 0.7244 (pp20) cc_final: 0.7027 (pp20) REVERT: B 234 ASN cc_start: 0.7787 (m-40) cc_final: 0.7502 (t0) REVERT: D 51 SER cc_start: 0.8341 (m) cc_final: 0.7993 (t) REVERT: E 35 GLN cc_start: 0.7801 (mp10) cc_final: 0.7076 (mp10) REVERT: E 55 TYR cc_start: 0.8731 (m-80) cc_final: 0.8358 (m-80) REVERT: F 17 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7834 (mmmt) REVERT: F 37 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7514 (mt-10) REVERT: F 45 LEU cc_start: 0.8016 (mp) cc_final: 0.7482 (tt) REVERT: G 17 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8228 (mtmt) REVERT: G 35 GLN cc_start: 0.8402 (mt0) cc_final: 0.8052 (mt0) REVERT: G 47 LYS cc_start: 0.8304 (tmtp) cc_final: 0.7958 (tttp) REVERT: H 40 ASP cc_start: 0.7886 (m-30) cc_final: 0.7611 (m-30) REVERT: J 36 ILE cc_start: 0.9178 (tt) cc_final: 0.8834 (mp) REVERT: L 68 VAL cc_start: 0.6985 (t) cc_final: 0.6643 (p) REVERT: M 47 LYS cc_start: 0.8565 (ttpm) cc_final: 0.8311 (ttpt) outliers start: 2 outliers final: 2 residues processed: 397 average time/residue: 0.3056 time to fit residues: 162.6687 Evaluate side-chains 263 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain I residue 9 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 96 GLN A 184 ASN B 7 ASN B 24 GLN B 136 GLN B 214 ASN E 8 GLN E 33 GLN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 13 ASN H 48 ASN I 33 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN J 52 GLN K 8 GLN K 35 GLN K 48 ASN L 48 ASN L 52 GLN M 28 ASN N 41 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105919 restraints weight = 46527.731| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.37 r_work: 0.3119 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11761 Z= 0.152 Angle : 0.672 9.100 16127 Z= 0.349 Chirality : 0.049 0.168 1845 Planarity : 0.007 0.111 1926 Dihedral : 11.345 73.886 1939 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.88 % Rotamer: Outliers : 1.33 % Allowed : 9.59 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.22), residues: 1289 helix: -1.68 (0.29), residues: 263 sheet: -1.77 (0.22), residues: 459 loop : -0.69 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 239 TYR 0.009 0.001 TYR A 145 PHE 0.013 0.001 PHE F 39 TRP 0.019 0.002 TRP A 217 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (11761) covalent geometry : angle 0.67163 / 0.35 (16127) hydrogen bonds : bond 0.05362 / 3.47 ( 409) hydrogen bonds : angle 6.25232 / 4.18 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 0.674 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 41 PHE cc_start: 0.7893 (t80) cc_final: 0.7585 (t80) REVERT: A 135 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7559 (tptp) REVERT: A 139 LYS cc_start: 0.9001 (mttt) cc_final: 0.8738 (mttm) REVERT: A 225 THR cc_start: 0.9351 (m) cc_final: 0.9125 (p) REVERT: B 64 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8306 (mp0) REVERT: B 134 SER cc_start: 0.9134 (t) cc_final: 0.8806 (p) REVERT: B 135 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7546 (tptp) REVERT: B 211 GLU cc_start: 0.7379 (pp20) cc_final: 0.7124 (tm-30) REVERT: E 35 GLN cc_start: 0.8051 (mp10) cc_final: 0.7361 (mp10) REVERT: E 55 TYR cc_start: 0.8938 (m-80) cc_final: 0.8509 (m-80) REVERT: G 35 GLN cc_start: 0.8748 (mt0) cc_final: 0.8453 (mt0) REVERT: I 19 ARG cc_start: 0.7228 (mtt90) cc_final: 0.6916 (mmt-90) REVERT: J 36 ILE cc_start: 0.9228 (tt) cc_final: 0.8752 (mp) REVERT: L 66 ARG cc_start: 0.8137 (ptt90) cc_final: 0.7918 (ptt90) REVERT: M 18 GLU cc_start: 0.7871 (mp0) cc_final: 0.7586 (mp0) REVERT: N 60 SER cc_start: 0.9061 (t) cc_final: 0.8650 (p) outliers start: 16 outliers final: 8 residues processed: 288 average time/residue: 0.3050 time to fit residues: 117.4770 Evaluate side-chains 245 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 237 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 ASN B 184 ASN C 28 ASN D 41 GLN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.101521 restraints weight = 46789.211| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.34 r_work: 0.3032 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11761 Z= 0.197 Angle : 0.618 7.250 16127 Z= 0.322 Chirality : 0.047 0.163 1845 Planarity : 0.006 0.099 1926 Dihedral : 11.079 73.933 1937 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 1.42 % Allowed : 11.26 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -1.53 (0.23), residues: 1289 helix: -0.87 (0.33), residues: 263 sheet: -1.50 (0.23), residues: 451 loop : -0.40 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.009 0.001 TYR K 55 PHE 0.013 0.001 PHE F 39 TRP 0.013 0.001 TRP A 217 HIS 0.006 0.001 HIS I 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (11761) covalent geometry : angle 0.61782 / 0.32 (16127) hydrogen bonds : bond 0.04702 / 3.06 ( 409) hydrogen bonds : angle 5.70022 / 3.84 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7699 (tptp) REVERT: A 139 LYS cc_start: 0.9048 (mttt) cc_final: 0.8756 (mttm) REVERT: A 225 THR cc_start: 0.9409 (m) cc_final: 0.9138 (p) REVERT: B 64 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8308 (mp0) REVERT: B 134 SER cc_start: 0.9119 (t) cc_final: 0.8805 (p) REVERT: B 135 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7575 (tptp) REVERT: D 23 SER cc_start: 0.9007 (p) cc_final: 0.8716 (t) REVERT: E 35 GLN cc_start: 0.8064 (mp10) cc_final: 0.7409 (mp10) REVERT: F 31 LYS cc_start: 0.8331 (ttpm) cc_final: 0.7903 (tttm) REVERT: G 35 GLN cc_start: 0.8823 (mt0) cc_final: 0.8527 (mt0) REVERT: I 19 ARG cc_start: 0.7235 (mtt90) cc_final: 0.6922 (mmt-90) REVERT: J 13 ASN cc_start: 0.8196 (m-40) cc_final: 0.7948 (m110) REVERT: J 18 GLU cc_start: 0.8353 (pp20) cc_final: 0.7707 (pp20) REVERT: J 36 ILE cc_start: 0.9233 (tt) cc_final: 0.8739 (mp) REVERT: K 9 ASP cc_start: 0.8546 (m-30) cc_final: 0.8158 (m-30) REVERT: L 66 ARG cc_start: 0.8354 (ptt90) cc_final: 0.8058 (ptt90) REVERT: L 68 VAL cc_start: 0.7060 (t) cc_final: 0.6831 (t) REVERT: M 9 ASP cc_start: 0.8332 (m-30) cc_final: 0.8120 (m-30) outliers start: 17 outliers final: 15 residues processed: 266 average time/residue: 0.2921 time to fit residues: 104.9600 Evaluate side-chains 257 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN B 9 ASN D 57 HIS E 28 ASN E 48 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 GLN L 57 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096041 restraints weight = 47201.050| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.34 r_work: 0.2971 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11761 Z= 0.300 Angle : 0.657 6.417 16127 Z= 0.344 Chirality : 0.050 0.185 1845 Planarity : 0.006 0.090 1926 Dihedral : 11.073 74.111 1937 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 2.25 % Allowed : 11.84 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.24), residues: 1289 helix: -0.47 (0.34), residues: 251 sheet: -1.35 (0.23), residues: 454 loop : -0.34 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 66 TYR 0.014 0.001 TYR K 55 PHE 0.015 0.002 PHE A 125 TRP 0.020 0.002 TRP B 217 HIS 0.008 0.002 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.30 (11761) covalent geometry : angle 0.65657 / 0.34 (16127) hydrogen bonds : bond 0.04866 / 3.19 ( 409) hydrogen bonds : angle 5.47399 / 3.70 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7758 (tptp) REVERT: A 139 LYS cc_start: 0.9082 (mttt) cc_final: 0.8831 (mttm) REVERT: A 206 ASP cc_start: 0.7149 (m-30) cc_final: 0.6815 (m-30) REVERT: B 134 SER cc_start: 0.9142 (t) cc_final: 0.8839 (p) REVERT: B 191 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8830 (tt) REVERT: D 51 SER cc_start: 0.8298 (m) cc_final: 0.7931 (t) REVERT: E 18 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 35 GLN cc_start: 0.8130 (mp10) cc_final: 0.7414 (mp10) REVERT: G 35 GLN cc_start: 0.8928 (mt0) cc_final: 0.8631 (mt0) REVERT: I 19 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6929 (mmt-90) REVERT: J 18 GLU cc_start: 0.8226 (pp20) cc_final: 0.7623 (pp20) REVERT: K 9 ASP cc_start: 0.8557 (m-30) cc_final: 0.8189 (m-30) REVERT: L 66 ARG cc_start: 0.8479 (ptt90) cc_final: 0.8198 (ptt90) REVERT: M 9 ASP cc_start: 0.8340 (m-30) cc_final: 0.8100 (m-30) outliers start: 27 outliers final: 23 residues processed: 259 average time/residue: 0.2828 time to fit residues: 99.1651 Evaluate side-chains 250 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 41 GLN D 52 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097944 restraints weight = 46566.901| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.33 r_work: 0.2998 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11761 Z= 0.156 Angle : 0.582 7.168 16127 Z= 0.301 Chirality : 0.047 0.180 1845 Planarity : 0.005 0.080 1926 Dihedral : 10.881 73.692 1935 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.03 % Rotamer: Outliers : 1.83 % Allowed : 12.26 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -1.16 (0.24), residues: 1289 helix: -0.35 (0.33), residues: 263 sheet: -1.34 (0.23), residues: 452 loop : -0.23 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 66 TYR 0.010 0.001 TYR B 221 PHE 0.010 0.001 PHE A 85 TRP 0.014 0.001 TRP B 217 HIS 0.005 0.001 HIS L 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (11761) covalent geometry : angle 0.58198 / 0.30 (16127) hydrogen bonds : bond 0.04114 / 2.68 ( 409) hydrogen bonds : angle 5.25035 / 3.57 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7762 (tptp) REVERT: A 139 LYS cc_start: 0.9043 (mttt) cc_final: 0.8749 (mttm) REVERT: A 206 ASP cc_start: 0.7278 (m-30) cc_final: 0.6927 (m-30) REVERT: A 225 THR cc_start: 0.9465 (m) cc_final: 0.9145 (p) REVERT: B 64 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8258 (mp0) REVERT: B 134 SER cc_start: 0.9083 (t) cc_final: 0.8863 (p) REVERT: B 197 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7758 (mt-10) REVERT: E 18 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7397 (tm-30) REVERT: E 35 GLN cc_start: 0.8070 (mp10) cc_final: 0.7367 (mp10) REVERT: G 35 GLN cc_start: 0.8924 (mt0) cc_final: 0.8661 (mt0) REVERT: J 18 GLU cc_start: 0.8372 (pp20) cc_final: 0.7751 (pp20) REVERT: K 9 ASP cc_start: 0.8574 (m-30) cc_final: 0.8172 (m-30) REVERT: L 66 ARG cc_start: 0.8424 (ptt90) cc_final: 0.8169 (ptt90) REVERT: M 9 ASP cc_start: 0.8293 (m-30) cc_final: 0.8082 (m-30) outliers start: 22 outliers final: 16 residues processed: 260 average time/residue: 0.2943 time to fit residues: 103.1593 Evaluate side-chains 244 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 ASN D 41 GLN E 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099663 restraints weight = 46737.817| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.36 r_work: 0.3016 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11761 Z= 0.115 Angle : 0.557 6.794 16127 Z= 0.286 Chirality : 0.046 0.170 1845 Planarity : 0.005 0.081 1926 Dihedral : 10.722 73.772 1935 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.72 % Rotamer: Outliers : 1.42 % Allowed : 13.34 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -1.00 (0.24), residues: 1289 helix: -0.19 (0.34), residues: 263 sheet: -1.34 (0.23), residues: 452 loop : -0.04 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.008 0.001 TYR K 55 PHE 0.013 0.001 PHE B 123 TRP 0.010 0.001 TRP B 217 HIS 0.005 0.001 HIS L 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (11761) covalent geometry : angle 0.55701 / 0.29 (16127) hydrogen bonds : bond 0.03776 / 2.45 ( 409) hydrogen bonds : angle 5.11289 / 3.48 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.9035 (mttt) cc_final: 0.8741 (mttm) REVERT: A 206 ASP cc_start: 0.7268 (m-30) cc_final: 0.6914 (m-30) REVERT: A 225 THR cc_start: 0.9494 (m) cc_final: 0.9150 (p) REVERT: B 35 ASP cc_start: 0.8603 (t0) cc_final: 0.8394 (t0) REVERT: B 64 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8308 (mp0) REVERT: B 179 ASP cc_start: 0.8971 (m-30) cc_final: 0.8763 (m-30) REVERT: B 191 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8826 (tt) REVERT: B 197 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7832 (mt-10) REVERT: E 18 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7423 (tm-30) REVERT: E 35 GLN cc_start: 0.8034 (mp10) cc_final: 0.7331 (mp10) REVERT: G 35 GLN cc_start: 0.8906 (mt0) cc_final: 0.8649 (mt0) REVERT: I 19 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7045 (mmt-90) REVERT: J 18 GLU cc_start: 0.8278 (pp20) cc_final: 0.7678 (pp20) REVERT: K 9 ASP cc_start: 0.8574 (m-30) cc_final: 0.8182 (m-30) REVERT: L 66 ARG cc_start: 0.8429 (ptt90) cc_final: 0.8175 (ptt90) REVERT: M 9 ASP cc_start: 0.8289 (m-30) cc_final: 0.8087 (m-30) outliers start: 17 outliers final: 12 residues processed: 248 average time/residue: 0.2804 time to fit residues: 94.8385 Evaluate side-chains 242 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 0.0040 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 ASN D 41 GLN E 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099042 restraints weight = 46850.730| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.24 r_work: 0.3001 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11761 Z= 0.176 Angle : 0.567 6.498 16127 Z= 0.293 Chirality : 0.046 0.169 1845 Planarity : 0.005 0.076 1926 Dihedral : 10.695 73.877 1935 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.88 % Rotamer: Outliers : 1.58 % Allowed : 13.51 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -0.92 (0.24), residues: 1289 helix: -0.05 (0.33), residues: 275 sheet: -1.27 (0.24), residues: 450 loop : -0.05 (0.29), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 66 TYR 0.018 0.001 TYR L 55 PHE 0.011 0.001 PHE A 123 TRP 0.014 0.001 TRP B 217 HIS 0.005 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (11761) covalent geometry : angle 0.56686 / 0.29 (16127) hydrogen bonds : bond 0.03996 / 2.61 ( 409) hydrogen bonds : angle 5.01169 / 3.41 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8828 (m-30) cc_final: 0.8463 (m-30) REVERT: A 135 LYS cc_start: 0.8470 (mtmt) cc_final: 0.7831 (tptp) REVERT: A 139 LYS cc_start: 0.9040 (mttt) cc_final: 0.8798 (mttm) REVERT: A 206 ASP cc_start: 0.7258 (m-30) cc_final: 0.6968 (m-30) REVERT: B 64 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8505 (mm-30) REVERT: B 191 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8921 (tt) REVERT: B 197 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7987 (mt-10) REVERT: E 18 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7391 (tm-30) REVERT: E 35 GLN cc_start: 0.8058 (mp10) cc_final: 0.7513 (mt0) REVERT: G 35 GLN cc_start: 0.8954 (mt0) cc_final: 0.8685 (mt0) REVERT: I 19 ARG cc_start: 0.7391 (mtt90) cc_final: 0.7053 (mmt-90) REVERT: J 18 GLU cc_start: 0.8253 (pp20) cc_final: 0.7651 (pp20) REVERT: K 9 ASP cc_start: 0.8560 (m-30) cc_final: 0.8150 (m-30) REVERT: K 37 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8328 (mt-10) REVERT: L 66 ARG cc_start: 0.8446 (ptt90) cc_final: 0.8218 (ptt90) REVERT: M 9 ASP cc_start: 0.8303 (m-30) cc_final: 0.8089 (m-30) outliers start: 19 outliers final: 17 residues processed: 252 average time/residue: 0.2903 time to fit residues: 98.8926 Evaluate side-chains 249 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 ASN D 41 GLN ** I 52 GLN ** 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 = 0.3450 r_free = 0.3450 target = 0.121512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098346 restraints weight = 46611.095| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.34 r_work: 0.3009 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11761 Z= 0.123 Angle : 0.553 6.854 16127 Z= 0.284 Chirality : 0.046 0.170 1845 Planarity : 0.005 0.076 1926 Dihedral : 10.603 73.687 1935 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.72 % Rotamer: Outliers : 1.08 % Allowed : 14.60 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -0.82 (0.25), residues: 1289 helix: 0.04 (0.33), residues: 275 sheet: -1.26 (0.24), residues: 450 loop : 0.05 (0.29), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.010 0.001 TYR K 55 PHE 0.011 0.001 PHE B 123 TRP 0.011 0.001 TRP B 217 HIS 0.004 0.001 HIS L 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (11761) covalent geometry : angle 0.55346 / 0.28 (16127) hydrogen bonds : bond 0.03672 / 2.39 ( 409) hydrogen bonds : angle 4.92871 / 3.36 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8829 (m-30) cc_final: 0.8457 (m-30) REVERT: A 139 LYS cc_start: 0.9027 (mttt) cc_final: 0.8785 (mttm) REVERT: A 206 ASP cc_start: 0.7279 (m-30) cc_final: 0.6989 (m-30) REVERT: A 225 THR cc_start: 0.9490 (m) cc_final: 0.9247 (p) REVERT: B 64 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8503 (mm-30) REVERT: E 18 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 35 GLN cc_start: 0.8040 (mp10) cc_final: 0.7485 (mt0) REVERT: G 35 GLN cc_start: 0.8926 (mt0) cc_final: 0.8653 (mt0) REVERT: J 18 GLU cc_start: 0.8253 (pp20) cc_final: 0.7652 (pp20) REVERT: K 9 ASP cc_start: 0.8559 (m-30) cc_final: 0.8157 (m-30) REVERT: K 37 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8243 (mt-10) REVERT: L 52 GLN cc_start: 0.8459 (tt0) cc_final: 0.8093 (tt0) REVERT: L 66 ARG cc_start: 0.8499 (ptt90) cc_final: 0.8270 (ptt90) REVERT: M 9 ASP cc_start: 0.8340 (m-30) cc_final: 0.8102 (m-30) REVERT: N 18 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8007 (mt-10) outliers start: 13 outliers final: 13 residues processed: 250 average time/residue: 0.2866 time to fit residues: 97.6014 Evaluate side-chains 245 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 ASN D 41 GLN ** I 52 GLN ** 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 = 0.3456 r_free = 0.3456 target = 0.121979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.098727 restraints weight = 46886.616| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.35 r_work: 0.3014 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11761 Z= 0.115 Angle : 0.544 6.854 16127 Z= 0.279 Chirality : 0.046 0.163 1845 Planarity : 0.005 0.075 1926 Dihedral : 10.516 73.709 1935 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.88 % Rotamer: Outliers : 1.25 % Allowed : 14.85 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.25), residues: 1289 helix: 0.21 (0.33), residues: 275 sheet: -1.25 (0.24), residues: 448 loop : 0.09 (0.29), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 19 TYR 0.013 0.001 TYR F 55 PHE 0.010 0.001 PHE A 123 TRP 0.010 0.001 TRP B 217 HIS 0.004 0.001 HIS L 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (11761) covalent geometry : angle 0.54394 / 0.28 (16127) hydrogen bonds : bond 0.03556 / 2.31 ( 409) hydrogen bonds : angle 4.84143 / 3.31 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8806 (m-30) cc_final: 0.8430 (m-30) REVERT: A 139 LYS cc_start: 0.9027 (mttt) cc_final: 0.8773 (mttm) REVERT: A 206 ASP cc_start: 0.7269 (m-30) cc_final: 0.6976 (m-30) REVERT: A 225 THR cc_start: 0.9485 (m) cc_final: 0.9254 (p) REVERT: E 18 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7353 (tm-30) REVERT: E 35 GLN cc_start: 0.8020 (mp10) cc_final: 0.7475 (mt0) REVERT: G 35 GLN cc_start: 0.8923 (mt0) cc_final: 0.8651 (mt0) REVERT: J 18 GLU cc_start: 0.8104 (pp20) cc_final: 0.7675 (pp20) REVERT: K 9 ASP cc_start: 0.8546 (m-30) cc_final: 0.8135 (m-30) REVERT: K 37 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8273 (mt-10) REVERT: L 66 ARG cc_start: 0.8400 (ptt90) cc_final: 0.8196 (ptt90) REVERT: M 9 ASP cc_start: 0.8365 (m-30) cc_final: 0.8137 (m-30) REVERT: N 18 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7999 (mt-10) outliers start: 15 outliers final: 14 residues processed: 250 average time/residue: 0.2981 time to fit residues: 101.1468 Evaluate side-chains 247 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 ASN D 41 GLN G 5 HIS ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101629 restraints weight = 46315.158| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.24 r_work: 0.3054 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11761 Z= 0.097 Angle : 0.535 7.121 16127 Z= 0.272 Chirality : 0.045 0.163 1845 Planarity : 0.005 0.076 1926 Dihedral : 10.395 73.601 1935 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.88 % Rotamer: Outliers : 0.75 % Allowed : 15.43 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -0.58 (0.25), residues: 1289 helix: 0.37 (0.33), residues: 275 sheet: -1.25 (0.24), residues: 444 loop : 0.23 (0.30), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 19 TYR 0.008 0.001 TYR B 145 PHE 0.013 0.001 PHE B 123 TRP 0.008 0.001 TRP B 217 HIS 0.003 0.001 HIS L 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (11761) covalent geometry : angle 0.53491 / 0.27 (16127) hydrogen bonds : bond 0.03303 / 2.13 ( 409) hydrogen bonds : angle 4.74256 / 3.25 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 247 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8805 (m-30) cc_final: 0.8451 (m-30) REVERT: A 135 LYS cc_start: 0.8641 (ttmm) cc_final: 0.7409 (tptp) REVERT: A 139 LYS cc_start: 0.9019 (mttt) cc_final: 0.8771 (mttm) REVERT: A 206 ASP cc_start: 0.7283 (m-30) cc_final: 0.7002 (m-30) REVERT: A 225 THR cc_start: 0.9418 (m) cc_final: 0.9204 (p) REVERT: E 18 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7333 (tm-30) REVERT: E 35 GLN cc_start: 0.7994 (mp10) cc_final: 0.7463 (mt0) REVERT: G 35 GLN cc_start: 0.8892 (mt0) cc_final: 0.8618 (mt0) REVERT: J 18 GLU cc_start: 0.8248 (pp20) cc_final: 0.7822 (pp20) REVERT: K 9 ASP cc_start: 0.8535 (m-30) cc_final: 0.8131 (m-30) REVERT: K 37 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8264 (mt-10) REVERT: L 52 GLN cc_start: 0.8455 (tt0) cc_final: 0.8125 (tt0) REVERT: L 66 ARG cc_start: 0.8376 (ptt90) cc_final: 0.8157 (ptt90) REVERT: M 41 GLN cc_start: 0.8942 (pp30) cc_final: 0.8249 (pp30) REVERT: N 18 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7927 (mt-10) outliers start: 9 outliers final: 9 residues processed: 252 average time/residue: 0.3080 time to fit residues: 104.0634 Evaluate side-chains 247 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN B 9 ASN D 41 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095536 restraints weight = 47336.349| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.33 r_work: 0.2963 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11761 Z= 0.271 Angle : 0.615 6.709 16127 Z= 0.317 Chirality : 0.048 0.171 1845 Planarity : 0.005 0.077 1926 Dihedral : 10.555 73.989 1935 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 1.33 % Allowed : 15.35 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.08 % 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: -0.66 (0.25), residues: 1289 helix: 0.30 (0.33), residues: 275 sheet: -1.20 (0.23), residues: 452 loop : 0.11 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 66 TYR 0.026 0.001 TYR K 55 PHE 0.013 0.002 PHE A 123 TRP 0.020 0.002 TRP B 217 HIS 0.009 0.002 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 (11761) covalent geometry : angle 0.61485 / 0.32 (16127) hydrogen bonds : bond 0.04210 / 2.76 ( 409) hydrogen bonds : angle 4.89914 / 3.34 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5658.29 seconds wall clock time: 96 minutes 47.47 seconds (5807.47 seconds total)