Starting phenix.real_space_refine on Thu Mar 5 12:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1k_0590/03_2026/6o1k_0590_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1k_0590/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6o1k_0590/03_2026/6o1k_0590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1k_0590/03_2026/6o1k_0590.map" model { file = "/net/cci-nas-00/data/ceres_data/6o1k_0590/03_2026/6o1k_0590_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1k_0590/03_2026/6o1k_0590_neut.cif" } 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-dev-5986/lib/python3.9/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: 3.61, per 1000 atoms: 0.16 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: 1.57 Conformation dependent library (CDL) restraints added in 632.0 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: 3.81 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: 4.94 Time building geometry restraints manager: 2.27 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: 1403 0.066 - 0.131: 344 0.131 - 0.197: 74 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: 0.470 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: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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= 0.321 Angle : 1.060 12.333 16127 Z= 0.633 Chirality : 0.064 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 covalent geometry : bond 0.00557 (11761) covalent geometry : angle 1.05983 (16127) hydrogen bonds : bond 0.17923 ( 409) hydrogen bonds : angle 8.30525 ( 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 : 0.510 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: 0.8912 (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: 0.7835 (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: 0.7483 (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: 0.3110 time to fit residues: 162.3835 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 : 0.537 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 96 GLN A 184 ASN B 7 ASN B 24 GLN B 131 HIS B 136 GLN B 214 ASN E 8 GLN E 33 GLN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 48 ASN L 48 ASN L 52 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.105447 restraints weight = 46319.055| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.37 r_work: 0.3098 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11761 Z= 0.134 Angle : 0.604 7.335 16127 Z= 0.312 Chirality : 0.046 0.153 1845 Planarity : 0.006 0.099 1926 Dihedral : 11.101 73.789 1939 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 1.25 % Allowed : 9.17 % Favored : 89.57 % 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: -1.76 (0.22), residues: 1289 helix: -1.32 (0.30), residues: 263 sheet: -1.63 (0.22), residues: 434 loop : -0.46 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 16 TYR 0.010 0.001 TYR K 55 PHE 0.010 0.001 PHE A 243 TRP 0.017 0.001 TRP A 217 HIS 0.005 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00306 (11761) covalent geometry : angle 0.60435 (16127) hydrogen bonds : bond 0.04301 ( 409) hydrogen bonds : angle 5.70579 ( 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 305 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 290 time to evaluate : 0.478 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: A 41 PHE cc_start: 0.7980 (t80) cc_final: 0.7674 (t80) REVERT: A 135 LYS cc_start: 0.8410 (mtmt) cc_final: 0.7686 (tptp) REVERT: A 139 LYS cc_start: 0.9002 (mttt) cc_final: 0.8719 (mttm) REVERT: A 225 THR cc_start: 0.9355 (m) cc_final: 0.9133 (p) REVERT: B 35 ASP cc_start: 0.8494 (t70) cc_final: 0.8247 (t0) REVERT: B 64 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8320 (mp0) REVERT: B 135 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7595 (tptp) REVERT: E 35 GLN cc_start: 0.8015 (mp10) cc_final: 0.7395 (mp10) REVERT: F 17 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7668 (mmmt) REVERT: G 35 GLN cc_start: 0.8754 (mt0) cc_final: 0.8463 (mt0) REVERT: I 19 ARG cc_start: 0.7300 (mtt90) cc_final: 0.6995 (mmt-90) REVERT: J 31 LYS cc_start: 0.8275 (ptmt) cc_final: 0.7891 (ptmt) REVERT: J 36 ILE cc_start: 0.9197 (tt) cc_final: 0.8744 (mp) REVERT: K 9 ASP cc_start: 0.8575 (m-30) cc_final: 0.8009 (m-30) REVERT: L 66 ARG cc_start: 0.8374 (ptt90) cc_final: 0.8081 (ptt90) REVERT: N 35 GLN cc_start: 0.8495 (mt0) cc_final: 0.8230 (mt0) outliers start: 15 outliers final: 9 residues processed: 301 average time/residue: 0.3166 time to fit residues: 124.8713 Evaluate side-chains 248 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 C residue 6 SER 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: 4.9990 chunk 107 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 184 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 57 HIS E 48 ASN F 8 GLN I 57 HIS J 8 GLN L 57 HIS M 5 HIS ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097714 restraints weight = 47088.110| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.36 r_work: 0.3000 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11761 Z= 0.219 Angle : 0.608 5.624 16127 Z= 0.317 Chirality : 0.048 0.178 1845 Planarity : 0.005 0.087 1926 Dihedral : 10.932 73.813 1937 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.96 % Rotamer: Outliers : 1.83 % Allowed : 11.68 % Favored : 86.49 % 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: -1.09 (0.24), residues: 1289 helix: -0.28 (0.35), residues: 251 sheet: -1.35 (0.23), residues: 454 loop : -0.14 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 16 TYR 0.014 0.001 TYR K 55 PHE 0.013 0.001 PHE A 125 TRP 0.020 0.002 TRP B 217 HIS 0.006 0.002 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00509 (11761) covalent geometry : angle 0.60809 (16127) hydrogen bonds : bond 0.04405 ( 409) hydrogen bonds : angle 5.26446 ( 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 281 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 0.372 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 41 PHE cc_start: 0.8090 (t80) cc_final: 0.7777 (t80) REVERT: A 124 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8166 (ttmm) REVERT: A 128 ASP cc_start: 0.8888 (m-30) cc_final: 0.8509 (m-30) REVERT: A 135 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7744 (tptp) REVERT: A 139 LYS cc_start: 0.9020 (mttt) cc_final: 0.8714 (mttm) REVERT: B 64 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8282 (mp0) REVERT: B 197 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7835 (mt-10) REVERT: E 35 GLN cc_start: 0.8104 (mp10) cc_final: 0.7441 (mp10) REVERT: F 13 ASN cc_start: 0.7950 (m-40) cc_final: 0.7745 (m-40) REVERT: F 17 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7638 (mmmt) REVERT: G 35 GLN cc_start: 0.8918 (mt0) cc_final: 0.8640 (mt0) REVERT: J 9 ASP cc_start: 0.8568 (m-30) cc_final: 0.8360 (m-30) REVERT: J 13 ASN cc_start: 0.8187 (m-40) cc_final: 0.7816 (m110) REVERT: J 18 GLU cc_start: 0.8267 (pp20) cc_final: 0.7699 (pp20) REVERT: L 66 ARG cc_start: 0.8463 (ptt90) cc_final: 0.8200 (ptt90) REVERT: M 9 ASP cc_start: 0.8306 (m-30) cc_final: 0.8038 (m-30) REVERT: M 18 GLU cc_start: 0.7743 (mp0) cc_final: 0.7517 (mp0) outliers start: 22 outliers final: 17 residues processed: 276 average time/residue: 0.3115 time to fit residues: 113.8459 Evaluate side-chains 253 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 21 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 38 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 9 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096913 restraints weight = 46987.527| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.34 r_work: 0.2987 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11761 Z= 0.179 Angle : 0.576 6.899 16127 Z= 0.298 Chirality : 0.046 0.167 1845 Planarity : 0.005 0.073 1926 Dihedral : 10.755 73.845 1935 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 2.34 % Allowed : 13.01 % Favored : 84.65 % 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: -0.86 (0.24), residues: 1289 helix: 0.03 (0.35), residues: 251 sheet: -1.29 (0.23), residues: 450 loop : 0.01 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.015 0.001 TYR K 55 PHE 0.009 0.001 PHE A 125 TRP 0.015 0.001 TRP B 217 HIS 0.005 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00412 (11761) covalent geometry : angle 0.57649 (16127) hydrogen bonds : bond 0.03961 ( 409) hydrogen bonds : angle 5.03510 ( 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 273 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8147 (t80) cc_final: 0.7841 (t80) REVERT: A 139 LYS cc_start: 0.9015 (mttt) cc_final: 0.8768 (mttm) REVERT: A 206 ASP cc_start: 0.7170 (m-30) cc_final: 0.6905 (m-30) REVERT: B 64 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8491 (mm-30) REVERT: B 197 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7837 (mt-10) REVERT: E 18 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7326 (tm-30) REVERT: E 35 GLN cc_start: 0.8089 (mp10) cc_final: 0.7539 (mt0) REVERT: G 35 GLN cc_start: 0.8948 (mt0) cc_final: 0.8681 (mt0) REVERT: G 47 LYS cc_start: 0.9045 (tptt) cc_final: 0.8785 (tptp) REVERT: J 13 ASN cc_start: 0.8209 (m-40) cc_final: 0.7981 (m110) REVERT: J 18 GLU cc_start: 0.8373 (pp20) cc_final: 0.7791 (pp20) REVERT: J 31 LYS cc_start: 0.8408 (ptmt) cc_final: 0.8061 (ptmt) REVERT: K 37 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8289 (mt-10) REVERT: L 52 GLN cc_start: 0.8512 (tt0) cc_final: 0.8215 (tt0) REVERT: L 66 ARG cc_start: 0.8491 (ptt90) cc_final: 0.8275 (ptt90) REVERT: M 9 ASP cc_start: 0.8314 (m-30) cc_final: 0.8104 (m-30) REVERT: M 18 GLU cc_start: 0.7736 (mp0) cc_final: 0.7399 (mp0) REVERT: M 41 GLN cc_start: 0.9117 (pp30) cc_final: 0.8443 (pp30) outliers start: 28 outliers final: 23 residues processed: 266 average time/residue: 0.3065 time to fit residues: 107.5030 Evaluate side-chains 254 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 60 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 M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 63 VAL 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: 3.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.099096 restraints weight = 46638.835| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.24 r_work: 0.3022 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11761 Z= 0.138 Angle : 0.546 6.231 16127 Z= 0.281 Chirality : 0.045 0.166 1845 Planarity : 0.005 0.079 1926 Dihedral : 10.579 73.776 1935 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.35 % Favored : 94.49 % Rotamer: Outliers : 2.17 % Allowed : 14.01 % 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: -0.84 (0.25), residues: 1289 helix: 0.10 (0.33), residues: 275 sheet: -1.30 (0.23), residues: 444 loop : 0.00 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 66 TYR 0.011 0.001 TYR K 55 PHE 0.007 0.001 PHE B 125 TRP 0.012 0.001 TRP B 217 HIS 0.004 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00320 (11761) covalent geometry : angle 0.54582 (16127) hydrogen bonds : bond 0.03665 ( 409) hydrogen bonds : angle 4.88259 ( 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 279 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 0.508 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 41 PHE cc_start: 0.8127 (t80) cc_final: 0.7825 (t80) REVERT: A 139 LYS cc_start: 0.9019 (mttt) cc_final: 0.8768 (mttm) REVERT: A 206 ASP cc_start: 0.7271 (m-30) cc_final: 0.6994 (m-30) REVERT: B 197 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7826 (mt-10) REVERT: E 18 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 35 GLN cc_start: 0.8055 (mp10) cc_final: 0.7519 (mt0) REVERT: F 13 ASN cc_start: 0.8156 (m110) cc_final: 0.7797 (m-40) REVERT: G 35 GLN cc_start: 0.8895 (mt0) cc_final: 0.8667 (mt0) REVERT: G 47 LYS cc_start: 0.9101 (tptt) cc_final: 0.8898 (tptp) REVERT: J 13 ASN cc_start: 0.8212 (m-40) cc_final: 0.7932 (m110) REVERT: J 18 GLU cc_start: 0.8254 (pp20) cc_final: 0.7621 (pp20) REVERT: J 47 LYS cc_start: 0.8237 (tttp) cc_final: 0.7825 (tttt) REVERT: K 37 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8273 (mt-10) REVERT: M 9 ASP cc_start: 0.8298 (m-30) cc_final: 0.8042 (m-30) REVERT: M 18 GLU cc_start: 0.7764 (mp0) cc_final: 0.7354 (mp0) REVERT: M 41 GLN cc_start: 0.9066 (pp30) cc_final: 0.8411 (pp30) outliers start: 26 outliers final: 21 residues processed: 272 average time/residue: 0.3088 time to fit residues: 110.4236 Evaluate side-chains 259 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 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 B residue 130 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain F residue 38 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 K residue 38 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 49 THR 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: 2.9990 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 9 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099850 restraints weight = 46878.650| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.26 r_work: 0.3013 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4621 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= 0.122 Angle : 0.537 6.323 16127 Z= 0.274 Chirality : 0.045 0.162 1845 Planarity : 0.005 0.075 1926 Dihedral : 10.405 73.704 1935 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.72 % Rotamer: Outliers : 2.42 % Allowed : 14.43 % Favored : 83.15 % 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: -0.61 (0.25), residues: 1289 helix: 0.37 (0.33), residues: 275 sheet: -1.23 (0.23), residues: 434 loop : 0.13 (0.30), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 66 TYR 0.012 0.001 TYR K 55 PHE 0.006 0.001 PHE A 85 TRP 0.011 0.001 TRP B 217 HIS 0.004 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00284 (11761) covalent geometry : angle 0.53693 (16127) hydrogen bonds : bond 0.03442 ( 409) hydrogen bonds : angle 4.75047 ( 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 282 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.605 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 41 PHE cc_start: 0.8111 (t80) cc_final: 0.7827 (t80) REVERT: A 135 LYS cc_start: 0.8668 (ttmm) cc_final: 0.7436 (tptp) REVERT: A 139 LYS cc_start: 0.9034 (mttt) cc_final: 0.8789 (mttm) REVERT: A 206 ASP cc_start: 0.7169 (m-30) cc_final: 0.6934 (m-30) REVERT: B 197 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 51 SER cc_start: 0.8355 (m) cc_final: 0.7936 (p) REVERT: E 18 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 35 GLN cc_start: 0.8031 (mp10) cc_final: 0.7488 (mt0) REVERT: F 13 ASN cc_start: 0.8180 (m110) cc_final: 0.7746 (m110) REVERT: G 35 GLN cc_start: 0.8910 (mt0) cc_final: 0.8648 (mt0) REVERT: G 47 LYS cc_start: 0.9003 (tptt) cc_final: 0.8781 (tptp) REVERT: J 13 ASN cc_start: 0.8232 (m-40) cc_final: 0.7936 (m110) REVERT: J 18 GLU cc_start: 0.8106 (pp20) cc_final: 0.7516 (pp20) REVERT: J 47 LYS cc_start: 0.8201 (tttp) cc_final: 0.7794 (tttt) REVERT: K 33 GLN cc_start: 0.8886 (tt0) cc_final: 0.8486 (mt0) REVERT: K 37 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8385 (mt-10) REVERT: L 52 GLN cc_start: 0.8442 (tt0) cc_final: 0.8182 (tt0) REVERT: M 9 ASP cc_start: 0.8386 (m-30) cc_final: 0.8151 (m-30) REVERT: M 41 GLN cc_start: 0.9061 (pp30) cc_final: 0.8463 (pp30) REVERT: N 18 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8145 (mt-10) outliers start: 29 outliers final: 27 residues processed: 275 average time/residue: 0.3130 time to fit residues: 113.5855 Evaluate side-chains 267 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 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 130 THR Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 9 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.094760 restraints weight = 47388.537| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.32 r_work: 0.2956 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11761 Z= 0.229 Angle : 0.593 6.832 16127 Z= 0.307 Chirality : 0.047 0.176 1845 Planarity : 0.005 0.075 1926 Dihedral : 10.571 73.695 1935 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.34 % Rotamer: Outliers : 3.09 % Allowed : 14.51 % Favored : 82.40 % 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: 0.32 (0.34), residues: 263 sheet: -1.20 (0.23), residues: 450 loop : 0.10 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.022 0.001 TYR K 55 PHE 0.010 0.001 PHE B 125 TRP 0.017 0.002 TRP B 217 HIS 0.005 0.001 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00539 (11761) covalent geometry : angle 0.59346 (16127) hydrogen bonds : bond 0.04071 ( 409) hydrogen bonds : angle 4.89171 ( 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 272 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8215 (t80) cc_final: 0.7938 (t80) REVERT: A 139 LYS cc_start: 0.9066 (mttt) cc_final: 0.8820 (mttm) REVERT: A 206 ASP cc_start: 0.7119 (m-30) cc_final: 0.6890 (m-30) REVERT: B 197 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7852 (mt-10) REVERT: D 51 SER cc_start: 0.8332 (m) cc_final: 0.7913 (p) REVERT: E 18 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7590 (tm-30) REVERT: E 35 GLN cc_start: 0.8052 (mp10) cc_final: 0.7691 (mt0) REVERT: F 13 ASN cc_start: 0.8189 (m110) cc_final: 0.7780 (m110) REVERT: G 35 GLN cc_start: 0.8890 (mt0) cc_final: 0.8661 (mt0) REVERT: G 47 LYS cc_start: 0.9029 (tptt) cc_final: 0.8822 (tptp) REVERT: G 66 ARG cc_start: 0.8308 (ptp90) cc_final: 0.7990 (ptm-80) REVERT: J 13 ASN cc_start: 0.8227 (m-40) cc_final: 0.7882 (m110) REVERT: J 18 GLU cc_start: 0.8225 (pp20) cc_final: 0.7572 (pp20) REVERT: J 31 LYS cc_start: 0.8459 (ptmt) cc_final: 0.8130 (ptmt) REVERT: K 37 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8453 (mt-10) REVERT: M 9 ASP cc_start: 0.8420 (m-30) cc_final: 0.8150 (m-30) REVERT: N 18 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8107 (mt-10) outliers start: 37 outliers final: 32 residues processed: 265 average time/residue: 0.2939 time to fit residues: 104.0088 Evaluate side-chains 266 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096429 restraints weight = 46882.379| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.31 r_work: 0.2980 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4909 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= 0.152 Angle : 0.553 6.585 16127 Z= 0.283 Chirality : 0.045 0.173 1845 Planarity : 0.005 0.072 1926 Dihedral : 10.439 73.747 1935 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.66 % Favored : 94.18 % Rotamer: Outliers : 2.25 % Allowed : 15.43 % Favored : 82.32 % 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: -0.61 (0.25), residues: 1289 helix: 0.41 (0.34), residues: 275 sheet: -1.21 (0.23), residues: 448 loop : 0.15 (0.30), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.012 0.001 TYR K 55 PHE 0.008 0.001 PHE B 123 TRP 0.012 0.001 TRP B 217 HIS 0.003 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00352 (11761) covalent geometry : angle 0.55267 (16127) hydrogen bonds : bond 0.03648 ( 409) hydrogen bonds : angle 4.78157 ( 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 268 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8149 (t80) cc_final: 0.7898 (t80) REVERT: A 139 LYS cc_start: 0.9046 (mttt) cc_final: 0.8769 (mttm) REVERT: A 206 ASP cc_start: 0.7097 (m-30) cc_final: 0.6864 (m-30) REVERT: B 197 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 51 SER cc_start: 0.8332 (m) cc_final: 0.7932 (p) REVERT: E 18 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 35 GLN cc_start: 0.8092 (mp10) cc_final: 0.7699 (mt0) REVERT: F 13 ASN cc_start: 0.8158 (m110) cc_final: 0.7724 (m110) REVERT: G 35 GLN cc_start: 0.8867 (mt0) cc_final: 0.8630 (mt0) REVERT: J 13 ASN cc_start: 0.8165 (m-40) cc_final: 0.7818 (m110) REVERT: J 18 GLU cc_start: 0.8212 (pp20) cc_final: 0.7592 (pp20) REVERT: J 31 LYS cc_start: 0.8447 (ptmt) cc_final: 0.8171 (ptmt) REVERT: K 37 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8480 (mt-10) REVERT: L 52 GLN cc_start: 0.8500 (tt0) cc_final: 0.8179 (tt0) REVERT: L 66 ARG cc_start: 0.8640 (ptt90) cc_final: 0.8434 (ptt90) REVERT: M 9 ASP cc_start: 0.8392 (m-30) cc_final: 0.8146 (m-30) REVERT: N 18 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8098 (mt-10) outliers start: 27 outliers final: 25 residues processed: 261 average time/residue: 0.3049 time to fit residues: 105.7396 Evaluate side-chains 259 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 9 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 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 = 0.3464 r_free = 0.3464 target = 0.122875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100062 restraints weight = 45870.442| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.25 r_work: 0.3025 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11761 Z= 0.099 Angle : 0.526 6.611 16127 Z= 0.267 Chirality : 0.044 0.158 1845 Planarity : 0.005 0.075 1926 Dihedral : 10.225 73.672 1935 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.27 % Rotamer: Outliers : 1.67 % Allowed : 16.60 % Favored : 81.73 % 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: -0.41 (0.25), residues: 1289 helix: 0.63 (0.34), residues: 275 sheet: -1.16 (0.24), residues: 444 loop : 0.30 (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 L 11 PHE 0.006 0.001 PHE B 123 TRP 0.008 0.001 TRP B 217 HIS 0.004 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00231 (11761) covalent geometry : angle 0.52595 (16127) hydrogen bonds : bond 0.03192 ( 409) hydrogen bonds : angle 4.61897 ( 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 279 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.624 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: A 41 PHE cc_start: 0.8133 (t80) cc_final: 0.7881 (t80) REVERT: A 139 LYS cc_start: 0.9006 (mttt) cc_final: 0.8752 (mttm) REVERT: A 206 ASP cc_start: 0.7088 (m-30) cc_final: 0.6797 (m-30) REVERT: B 197 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7799 (mt-10) REVERT: D 51 SER cc_start: 0.8326 (m) cc_final: 0.7922 (p) REVERT: E 31 LYS cc_start: 0.8378 (ptmt) cc_final: 0.8128 (ptmm) REVERT: E 35 GLN cc_start: 0.8095 (mp10) cc_final: 0.7706 (mt0) REVERT: F 13 ASN cc_start: 0.8085 (m110) cc_final: 0.7650 (m110) REVERT: G 35 GLN cc_start: 0.8803 (mt0) cc_final: 0.8567 (mt0) REVERT: G 66 ARG cc_start: 0.8299 (ptp90) cc_final: 0.7973 (ptm-80) REVERT: I 55 TYR cc_start: 0.8983 (m-80) cc_final: 0.8738 (m-80) REVERT: J 13 ASN cc_start: 0.8131 (m-40) cc_final: 0.7798 (m110) REVERT: J 18 GLU cc_start: 0.8280 (pp20) cc_final: 0.7468 (pp20) REVERT: J 47 LYS cc_start: 0.8184 (tttp) cc_final: 0.7785 (tttt) REVERT: K 33 GLN cc_start: 0.8858 (tt0) cc_final: 0.8486 (mt0) REVERT: L 52 GLN cc_start: 0.8459 (tt0) cc_final: 0.8135 (tt0) REVERT: L 66 ARG cc_start: 0.8569 (ptt90) cc_final: 0.8352 (ptt90) REVERT: M 9 ASP cc_start: 0.8338 (m-30) cc_final: 0.8090 (m-30) REVERT: M 16 ARG cc_start: 0.7472 (ttm170) cc_final: 0.7043 (ttp80) REVERT: M 41 GLN cc_start: 0.9028 (pp30) cc_final: 0.8443 (pp30) REVERT: N 18 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8117 (mt-10) outliers start: 20 outliers final: 19 residues processed: 274 average time/residue: 0.3046 time to fit residues: 111.1836 Evaluate side-chains 263 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain F residue 38 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 J residue 20 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 N residue 23 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: 3.9990 chunk 71 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 9 ASN B 234 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3455 r_free = 0.3455 target = 0.122221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099425 restraints weight = 45755.910| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.25 r_work: 0.3031 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11761 Z= 0.102 Angle : 0.532 6.437 16127 Z= 0.270 Chirality : 0.045 0.160 1845 Planarity : 0.005 0.069 1926 Dihedral : 10.149 73.585 1935 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.96 % Rotamer: Outliers : 1.67 % Allowed : 17.18 % Favored : 81.15 % 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: -0.32 (0.25), residues: 1289 helix: 0.74 (0.33), residues: 289 sheet: -1.21 (0.24), residues: 436 loop : 0.40 (0.31), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 19 TYR 0.008 0.001 TYR L 11 PHE 0.007 0.001 PHE A 85 TRP 0.009 0.001 TRP B 217 HIS 0.003 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00239 (11761) covalent geometry : angle 0.53160 (16127) hydrogen bonds : bond 0.03125 ( 409) hydrogen bonds : angle 4.55274 ( 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 265 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8122 (t80) cc_final: 0.7873 (t80) REVERT: A 139 LYS cc_start: 0.9006 (mttt) cc_final: 0.8757 (mttm) REVERT: A 206 ASP cc_start: 0.7153 (m-30) cc_final: 0.6878 (m-30) REVERT: B 197 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7799 (mt-10) REVERT: E 31 LYS cc_start: 0.8377 (ptmt) cc_final: 0.8132 (ptmm) REVERT: E 35 GLN cc_start: 0.8093 (mp10) cc_final: 0.7699 (mt0) REVERT: F 13 ASN cc_start: 0.8085 (m110) cc_final: 0.7645 (m110) REVERT: G 18 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7915 (mt-10) REVERT: G 35 GLN cc_start: 0.8784 (mt0) cc_final: 0.8547 (mt0) REVERT: G 66 ARG cc_start: 0.8302 (ptp90) cc_final: 0.7936 (ptm-80) REVERT: J 13 ASN cc_start: 0.8150 (m-40) cc_final: 0.7817 (m110) REVERT: J 18 GLU cc_start: 0.8235 (pp20) cc_final: 0.7495 (pp20) REVERT: J 31 LYS cc_start: 0.8335 (ptmt) cc_final: 0.8069 (ptmt) REVERT: J 47 LYS cc_start: 0.8053 (tttp) cc_final: 0.7645 (tttt) REVERT: K 33 GLN cc_start: 0.8850 (tt0) cc_final: 0.8510 (mt0) REVERT: L 52 GLN cc_start: 0.8453 (tt0) cc_final: 0.8156 (tt0) REVERT: L 66 ARG cc_start: 0.8556 (ptt90) cc_final: 0.8342 (ptt90) REVERT: M 9 ASP cc_start: 0.8355 (m-30) cc_final: 0.8103 (m-30) REVERT: M 16 ARG cc_start: 0.7448 (ttm170) cc_final: 0.7017 (ttp80) REVERT: M 41 GLN cc_start: 0.9022 (pp30) cc_final: 0.8443 (pp30) REVERT: N 18 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8122 (mt-10) outliers start: 20 outliers final: 20 residues processed: 260 average time/residue: 0.2994 time to fit residues: 104.0401 Evaluate side-chains 259 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 130 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 B residue 130 THR Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue 20 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 N residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 234 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.117332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.094570 restraints weight = 46489.680| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.25 r_work: 0.2965 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11761 Z= 0.219 Angle : 0.594 5.860 16127 Z= 0.305 Chirality : 0.047 0.178 1845 Planarity : 0.005 0.076 1926 Dihedral : 10.377 73.607 1935 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 1.92 % Allowed : 17.18 % Favored : 80.90 % 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: -0.45 (0.25), residues: 1289 helix: 0.67 (0.34), residues: 275 sheet: -1.18 (0.24), residues: 452 loop : 0.25 (0.30), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 90 TYR 0.018 0.001 TYR K 55 PHE 0.010 0.001 PHE B 125 TRP 0.017 0.001 TRP B 217 HIS 0.005 0.001 HIS K 57 Details of bonding type rmsd covalent geometry : bond 0.00516 (11761) covalent geometry : angle 0.59369 (16127) hydrogen bonds : bond 0.03899 ( 409) hydrogen bonds : angle 4.75125 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5808.50 seconds wall clock time: 98 minutes 57.28 seconds (5937.28 seconds total)