Starting phenix.real_space_refine on Fri Mar 6 12:08:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pww_20513/03_2026/6pww_20513.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pww_20513/03_2026/6pww_20513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pww_20513/03_2026/6pww_20513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pww_20513/03_2026/6pww_20513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pww_20513/03_2026/6pww_20513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pww_20513/03_2026/6pww_20513.map" } resolution = 4.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15700 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 52 5.16 5 C 10541 2.51 5 N 3308 2.21 5 O 3980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 18174 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2392 Chain: "C" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1228 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6089 SG CYS C3957 66.535 36.201 100.003 1.00788.66 S Time building chain proxies: 4.52, per 1000 atoms: 0.25 Number of scatterers: 18174 At special positions: 0 Unit cell: (136.35, 146.45, 123.22, 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) Zn 1 29.99 S 52 16.00 P 292 15.00 O 3980 8.00 N 3308 7.00 C 10541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 652.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C4002 " pdb="ZN ZN C4002 " - pdb=" SG CYS C3957 " 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 28 sheets defined 38.3% alpha, 20.7% beta 150 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 3815 through 3827 Processing helix chain 'C' and resid 3865 through 3879 removed outlier: 4.112A pdb=" N ASP C3869 " --> pdb=" O SER C3865 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS C3870 " --> pdb=" O ILE C3866 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C3878 " --> pdb=" O TYR C3874 " (cutoff:3.500A) Processing helix chain 'C' and resid 3901 through 3905 Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.768A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.422A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 101 through 120 Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.768A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 Processing helix chain 'M' and resid 16 through 22 removed outlier: 3.510A pdb=" N ARG M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.554A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 removed outlier: 3.634A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 120 removed outlier: 3.579A pdb=" N ALA N 104 " --> pdb=" O PRO N 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 30 through 42 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.939A pdb=" N VAL A 318 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 32 removed outlier: 4.213A pdb=" N THR A 29 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.511A pdb=" N ALA A 84 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 72 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 82 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP A 74 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 80 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 90 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN A 92 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 116 removed outlier: 6.532A pdb=" N CYS A 126 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 113 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 124 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR A 115 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS A 122 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 159 removed outlier: 6.896A pdb=" N ILE A 175 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 188 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 177 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 184 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 205 removed outlier: 3.595A pdb=" N THR A 217 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 270 removed outlier: 5.996A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.291A pdb=" N VAL A 343 " --> pdb=" O VAL C3862 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ARG C3864 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AB1, first strand: chain 'B' and resid 36 through 42 removed outlier: 5.619A pdb=" N LEU B 37 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 331 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 39 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 48 through 53 removed outlier: 5.760A pdb=" N GLY B 73 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE B 79 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 95 removed outlier: 6.563A pdb=" N ASP B 115 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 121 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.591A pdb=" N VAL B 153 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 166 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 155 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.510A pdb=" N ASP B 199 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N CYS B 205 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 217 through 222 removed outlier: 3.781A pdb=" N THR B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 238 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR B 251 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 240 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.781A pdb=" N VAL B 283 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 296 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 285 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3831 through 3835 Processing sheet with id=AB9, first strand: chain 'C' and resid 3854 through 3857 removed outlier: 7.168A pdb=" N MET C3854 " --> pdb=" O ALA C3930 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C3930 " --> pdb=" O MET C3854 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3906 through 3907 removed outlier: 5.908A pdb=" N ASN C3906 " --> pdb=" O TYR C3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.902A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AC4, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.236A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AC6, first strand: chain 'I' and resid 101 through 102 removed outlier: 7.549A pdb=" N THR I 101 " --> pdb=" O TYR L 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.864A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AC9, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.212A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'M' and resid 77 through 78 599 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 385 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4146 1.33 - 1.45: 5136 1.45 - 1.57: 9181 1.57 - 1.69: 582 1.69 - 1.81: 73 Bond restraints: 19118 Sorted by residual: bond pdb=" C2 SAH C4001 " pdb=" N3 SAH C4001 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" C8 SAH C4001 " pdb=" N7 SAH C4001 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C2 SAH C4001 " pdb=" N1 SAH C4001 " ideal model delta sigma weight residual 1.330 1.380 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C6 SAH C4001 " pdb=" N1 SAH C4001 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.55e+00 ... (remaining 19113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 26976 2.76 - 5.51: 128 5.51 - 8.27: 4 8.27 - 11.03: 4 11.03 - 13.78: 2 Bond angle restraints: 27114 Sorted by residual: angle pdb=" N VAL B 268 " pdb=" CA VAL B 268 " pdb=" C VAL B 268 " ideal model delta sigma weight residual 113.53 109.22 4.31 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N GLY J 101 " pdb=" CA GLY J 101 " pdb=" C GLY J 101 " ideal model delta sigma weight residual 110.77 117.75 -6.98 1.93e+00 2.68e-01 1.31e+01 angle pdb=" CG SAH C4001 " pdb=" SD SAH C4001 " pdb=" C5' SAH C4001 " ideal model delta sigma weight residual 101.77 91.53 10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" O SAH C4001 " pdb=" C SAH C4001 " pdb=" OXT SAH C4001 " ideal model delta sigma weight residual 126.79 116.93 9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C2 SAH C4001 " pdb=" N3 SAH C4001 " pdb=" C4 SAH C4001 " ideal model delta sigma weight residual 111.67 120.27 -8.60 3.00e+00 1.11e-01 8.23e+00 ... (remaining 27109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 9068 34.23 - 68.46: 1574 68.46 - 102.69: 41 102.69 - 136.92: 3 136.92 - 171.14: 2 Dihedral angle restraints: 10688 sinusoidal: 6195 harmonic: 4493 Sorted by residual: dihedral pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N TRP A 329 " pdb=" CA TRP A 329 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER A 196 " pdb=" C SER A 196 " pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ASN L 64 " pdb=" C ASN L 64 " pdb=" N VAL L 65 " pdb=" CA VAL L 65 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 10685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2190 0.038 - 0.076: 680 0.076 - 0.114: 174 0.114 - 0.152: 35 0.152 - 0.190: 1 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" C3' SAH C4001 " pdb=" C2' SAH C4001 " pdb=" C4' SAH C4001 " pdb=" O3' SAH C4001 " both_signs ideal model delta sigma weight residual False -2.71 -2.56 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE A 204 " pdb=" N ILE A 204 " pdb=" C ILE A 204 " pdb=" CB ILE A 204 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 3077 not shown) Planarity restraints: 2419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC O 54 " -0.000 2.00e-02 2.50e+03 1.43e-02 4.62e+00 pdb=" N1 DC O 54 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC O 54 " 0.037 2.00e-02 2.50e+03 pdb=" O2 DC O 54 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC O 54 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC O 54 " 0.006 2.00e-02 2.50e+03 pdb=" N4 DC O 54 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC O 54 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC O 54 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 110 " -0.011 2.00e-02 2.50e+03 1.30e-02 3.81e+00 pdb=" N1 DC O 110 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DC O 110 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC O 110 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DC O 110 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DC O 110 " -0.014 2.00e-02 2.50e+03 pdb=" N4 DC O 110 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC O 110 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC O 110 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 126 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 127 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.026 5.00e-02 4.00e+02 ... (remaining 2416 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 275 2.58 - 3.16: 15917 3.16 - 3.74: 36858 3.74 - 4.32: 46583 4.32 - 4.90: 67156 Nonbonded interactions: 166789 Sorted by model distance: nonbonded pdb=" N2 DG O 83 " pdb=" O2 DC P 65 " model vdw 1.996 2.496 nonbonded pdb=" OG1 THR A 217 " pdb=" OD1 ASP A 219 " model vdw 2.152 3.040 nonbonded pdb=" N CYS C3909 " pdb="ZN ZN C4002 " model vdw 2.172 2.310 nonbonded pdb=" O ILE C3905 " pdb=" OH TYR C3944 " model vdw 2.175 3.040 nonbonded pdb=" O PHE B 263 " pdb=" OG1 THR B 307 " model vdw 2.184 3.040 ... (remaining 166784 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 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 0.584 19120 Z= 0.244 Angle : 0.640 13.783 27114 Z= 0.374 Chirality : 0.040 0.190 3080 Planarity : 0.003 0.046 2419 Dihedral : 25.779 171.144 7786 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.22 % Allowed : 5.81 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.19), residues: 1523 helix: -0.53 (0.20), residues: 568 sheet: -2.40 (0.26), residues: 300 loop : -2.44 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 83 TYR 0.009 0.001 TYR A 225 PHE 0.009 0.001 PHE N 62 TRP 0.020 0.001 TRP A 329 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00414 (19118) covalent geometry : angle 0.63957 (27114) hydrogen bonds : bond 0.14153 ( 982) hydrogen bonds : angle 5.79919 ( 2479) metal coordination : bond 0.58448 ( 1) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 368 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 134 MET cc_start: 0.9370 (ttp) cc_final: 0.9040 (tmm) REVERT: A 242 MET cc_start: 0.9407 (ttm) cc_final: 0.9120 (ttp) REVERT: A 265 TYR cc_start: 0.9251 (m-80) cc_final: 0.9000 (m-80) REVERT: A 267 VAL cc_start: 0.9771 (p) cc_final: 0.9540 (m) REVERT: A 277 TYR cc_start: 0.9215 (m-10) cc_final: 0.8729 (m-80) REVERT: B 241 TRP cc_start: 0.7611 (m100) cc_final: 0.7352 (m-10) REVERT: C 3969 ASN cc_start: 0.6113 (m-40) cc_final: 0.5890 (m110) REVERT: G 50 GLU cc_start: 0.9590 (tp30) cc_final: 0.9277 (tp30) REVERT: G 58 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8504 (m) REVERT: G 60 LEU cc_start: 0.8577 (mm) cc_final: 0.7971 (mm) REVERT: G 62 ILE cc_start: 0.9673 (mt) cc_final: 0.9436 (mm) REVERT: G 70 LEU cc_start: 0.9731 (tp) cc_final: 0.9132 (tp) REVERT: G 73 GLU cc_start: 0.8870 (tt0) cc_final: 0.8662 (tt0) REVERT: G 77 ASP cc_start: 0.9152 (m-30) cc_final: 0.8831 (m-30) REVERT: G 97 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8501 (mt-10) REVERT: G 109 LEU cc_start: 0.9824 (OUTLIER) cc_final: 0.9607 (tt) REVERT: G 112 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9463 (mt) REVERT: G 133 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7563 (mt-10) REVERT: H 25 ASN cc_start: 0.8331 (m-40) cc_final: 0.7378 (t0) REVERT: H 72 TYR cc_start: 0.9359 (m-80) cc_final: 0.9075 (m-10) REVERT: H 88 TYR cc_start: 0.9404 (m-10) cc_final: 0.8932 (m-80) REVERT: H 98 TYR cc_start: 0.8792 (m-10) cc_final: 0.8385 (m-80) REVERT: I 41 GLU cc_start: 0.9319 (tt0) cc_final: 0.8814 (tm-30) REVERT: I 56 GLU cc_start: 0.9375 (tt0) cc_final: 0.8825 (mt-10) REVERT: I 63 LEU cc_start: 0.9552 (pp) cc_final: 0.9305 (pp) REVERT: I 64 GLU cc_start: 0.9633 (tt0) cc_final: 0.9334 (mm-30) REVERT: I 77 ARG cc_start: 0.9266 (mtm110) cc_final: 0.8983 (ttm-80) REVERT: I 83 LEU cc_start: 0.9677 (mp) cc_final: 0.9310 (mp) REVERT: I 91 GLU cc_start: 0.9547 (tm-30) cc_final: 0.9326 (tm-30) REVERT: I 95 LYS cc_start: 0.9646 (tptt) cc_final: 0.9380 (tppt) REVERT: J 59 MET cc_start: 0.9856 (mmm) cc_final: 0.9480 (mmm) REVERT: J 62 PHE cc_start: 0.9715 (t80) cc_final: 0.9453 (t80) REVERT: J 65 ASP cc_start: 0.9168 (t70) cc_final: 0.8610 (t0) REVERT: J 68 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8981 (tm-30) REVERT: J 76 ARG cc_start: 0.9434 (ttm110) cc_final: 0.9031 (ttm110) REVERT: J 96 ARG cc_start: 0.9346 (mtp180) cc_final: 0.9146 (mmm-85) REVERT: J 102 GLU cc_start: 0.9267 (tp30) cc_final: 0.8961 (tm-30) REVERT: J 103 LEU cc_start: 0.9619 (mt) cc_final: 0.9286 (mt) REVERT: K 41 TYR cc_start: 0.9041 (m-80) cc_final: 0.8612 (m-80) REVERT: K 50 GLU cc_start: 0.9060 (tp30) cc_final: 0.8670 (tp30) REVERT: K 61 LEU cc_start: 0.9489 (mm) cc_final: 0.9149 (mp) REVERT: K 65 LEU cc_start: 0.9768 (mm) cc_final: 0.9502 (mm) REVERT: K 73 GLU cc_start: 0.8731 (tt0) cc_final: 0.8434 (pt0) REVERT: K 82 LEU cc_start: 0.9417 (mt) cc_final: 0.9203 (mt) REVERT: K 97 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8477 (mt-10) REVERT: K 106 ASP cc_start: 0.8629 (p0) cc_final: 0.8350 (p0) REVERT: K 119 ILE cc_start: 0.8920 (pt) cc_final: 0.8698 (tp) REVERT: K 123 ASP cc_start: 0.8800 (t70) cc_final: 0.8143 (t70) REVERT: M 36 LYS cc_start: 0.9235 (mttm) cc_final: 0.8823 (mtmm) REVERT: M 56 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9167 (mt-10) REVERT: M 90 ASP cc_start: 0.9615 (t0) cc_final: 0.9381 (t70) REVERT: M 94 ASN cc_start: 0.9551 (t0) cc_final: 0.9299 (t0) REVERT: M 112 GLN cc_start: 0.9417 (mm-40) cc_final: 0.8360 (tm-30) REVERT: N 30 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8176 (mtt180) REVERT: N 59 MET cc_start: 0.9824 (mmm) cc_final: 0.9502 (tpt) REVERT: N 65 ASP cc_start: 0.9252 (t0) cc_final: 0.8836 (t0) REVERT: N 83 ARG cc_start: 0.9383 (mmp-170) cc_final: 0.8951 (mmp80) REVERT: N 92 GLN cc_start: 0.9482 (tt0) cc_final: 0.9221 (pp30) REVERT: N 96 ARG cc_start: 0.9537 (mtp180) cc_final: 0.9222 (tpp80) REVERT: N 98 LEU cc_start: 0.9038 (mt) cc_final: 0.8702 (mt) REVERT: N 105 LYS cc_start: 0.9668 (mttt) cc_final: 0.9359 (mmmt) REVERT: N 110 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8937 (mm-30) REVERT: L 74 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9120 (tm-30) REVERT: L 91 LYS cc_start: 0.9687 (tttt) cc_final: 0.9355 (mtpt) REVERT: L 97 LEU cc_start: 0.9703 (tp) cc_final: 0.9020 (tp) REVERT: L 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8366 (m-80) outliers start: 16 outliers final: 4 residues processed: 370 average time/residue: 0.1576 time to fit residues: 83.6842 Evaluate side-chains 264 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 257 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 285 ASN B 178 HIS B 265 ASN B 289 GLN B 310 HIS B 323 ASN G 39 HIS G 68 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 64 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN J 106 HIS ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS N 46 HIS N 60 ASN L 25 ASN L 64 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.041685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.028253 restraints weight = 171145.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.029608 restraints weight = 82002.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.030499 restraints weight = 48554.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.031041 restraints weight = 33065.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031490 restraints weight = 24968.840| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19120 Z= 0.182 Angle : 0.649 10.123 27114 Z= 0.365 Chirality : 0.042 0.305 3080 Planarity : 0.005 0.048 2419 Dihedral : 29.882 174.437 4880 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.21), residues: 1523 helix: 1.02 (0.21), residues: 588 sheet: -2.14 (0.26), residues: 304 loop : -2.05 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 52 TYR 0.012 0.001 TYR C3874 PHE 0.028 0.002 PHE K 67 TRP 0.022 0.002 TRP B 156 HIS 0.012 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00399 (19118) covalent geometry : angle 0.64853 (27114) hydrogen bonds : bond 0.06916 ( 982) hydrogen bonds : angle 4.60699 ( 2479) metal coordination : bond 0.00734 ( 1) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.574 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: A 134 MET cc_start: 0.9248 (ttp) cc_final: 0.8949 (tmm) REVERT: A 242 MET cc_start: 0.9499 (ttm) cc_final: 0.9186 (ttp) REVERT: A 265 TYR cc_start: 0.9302 (m-80) cc_final: 0.9062 (m-80) REVERT: C 3872 GLU cc_start: 0.5263 (mt-10) cc_final: 0.5039 (mt-10) REVERT: G 50 GLU cc_start: 0.9551 (tp30) cc_final: 0.9304 (tp30) REVERT: G 61 LEU cc_start: 0.9409 (mm) cc_final: 0.9165 (mm) REVERT: G 62 ILE cc_start: 0.9793 (mt) cc_final: 0.9565 (mm) REVERT: G 65 LEU cc_start: 0.9813 (mm) cc_final: 0.9428 (mm) REVERT: G 70 LEU cc_start: 0.9651 (tp) cc_final: 0.9171 (tp) REVERT: G 84 PHE cc_start: 0.9219 (m-80) cc_final: 0.8822 (m-10) REVERT: G 90 MET cc_start: 0.9615 (mmp) cc_final: 0.9274 (mmm) REVERT: G 97 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8690 (mt-10) REVERT: G 108 ASN cc_start: 0.9423 (t0) cc_final: 0.9154 (t0) REVERT: G 109 LEU cc_start: 0.9850 (tt) cc_final: 0.9643 (pp) REVERT: G 118 THR cc_start: 0.8991 (m) cc_final: 0.8626 (m) REVERT: G 125 GLN cc_start: 0.9724 (mt0) cc_final: 0.9408 (mm110) REVERT: G 130 ILE cc_start: 0.9745 (mm) cc_final: 0.9506 (mm) REVERT: H 25 ASN cc_start: 0.8249 (m-40) cc_final: 0.7522 (t0) REVERT: H 60 VAL cc_start: 0.9772 (t) cc_final: 0.9565 (t) REVERT: H 84 MET cc_start: 0.9086 (mmm) cc_final: 0.8675 (mmm) REVERT: H 85 ASP cc_start: 0.9144 (m-30) cc_final: 0.8898 (m-30) REVERT: H 88 TYR cc_start: 0.9431 (m-10) cc_final: 0.8764 (m-80) REVERT: I 41 GLU cc_start: 0.9347 (tt0) cc_final: 0.8749 (tm-30) REVERT: I 56 GLU cc_start: 0.9413 (tt0) cc_final: 0.8912 (mt-10) REVERT: I 64 GLU cc_start: 0.9631 (tt0) cc_final: 0.9011 (tp30) REVERT: I 83 LEU cc_start: 0.9716 (mp) cc_final: 0.9462 (pp) REVERT: I 95 LYS cc_start: 0.9629 (tptt) cc_final: 0.9334 (tppt) REVERT: I 111 ILE cc_start: 0.9495 (mm) cc_final: 0.9204 (mm) REVERT: I 112 GLN cc_start: 0.9252 (mp10) cc_final: 0.8603 (tm-30) REVERT: J 59 MET cc_start: 0.9688 (mmm) cc_final: 0.9424 (mmm) REVERT: J 62 PHE cc_start: 0.9678 (t80) cc_final: 0.9382 (t80) REVERT: J 65 ASP cc_start: 0.9230 (t70) cc_final: 0.9023 (t0) REVERT: J 76 ARG cc_start: 0.9576 (ttm110) cc_final: 0.9080 (ttm110) REVERT: J 91 ILE cc_start: 0.9861 (mp) cc_final: 0.9636 (tt) REVERT: J 92 GLN cc_start: 0.9700 (pt0) cc_final: 0.9335 (pp30) REVERT: J 96 ARG cc_start: 0.9475 (mtp180) cc_final: 0.9246 (mmm-85) REVERT: J 102 GLU cc_start: 0.9155 (tp30) cc_final: 0.8865 (tm-30) REVERT: J 103 LEU cc_start: 0.9628 (mt) cc_final: 0.9286 (mt) REVERT: K 41 TYR cc_start: 0.8994 (m-80) cc_final: 0.8740 (m-80) REVERT: K 50 GLU cc_start: 0.9127 (tp30) cc_final: 0.8111 (tp30) REVERT: K 54 TYR cc_start: 0.9094 (m-10) cc_final: 0.7696 (m-10) REVERT: K 61 LEU cc_start: 0.9451 (mm) cc_final: 0.9090 (mp) REVERT: K 80 THR cc_start: 0.9518 (p) cc_final: 0.9204 (p) REVERT: K 90 MET cc_start: 0.9491 (mmp) cc_final: 0.9285 (mmt) REVERT: K 93 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8585 (tm-30) REVERT: K 115 LYS cc_start: 0.9795 (mmmt) cc_final: 0.9494 (mmmm) REVERT: K 120 MET cc_start: 0.8843 (mtp) cc_final: 0.8384 (mtp) REVERT: K 123 ASP cc_start: 0.8147 (t70) cc_final: 0.7381 (t70) REVERT: K 124 ILE cc_start: 0.9788 (mp) cc_final: 0.9525 (mp) REVERT: M 38 ASN cc_start: 0.9471 (m110) cc_final: 0.9077 (p0) REVERT: M 64 GLU cc_start: 0.9259 (pp20) cc_final: 0.9024 (pp20) REVERT: M 94 ASN cc_start: 0.9765 (t0) cc_final: 0.9407 (m-40) REVERT: M 112 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9129 (mm110) REVERT: N 30 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7659 (mtt180) REVERT: N 64 ASN cc_start: 0.9847 (m-40) cc_final: 0.9643 (m-40) REVERT: N 65 ASP cc_start: 0.9368 (t0) cc_final: 0.8842 (t0) REVERT: N 92 GLN cc_start: 0.9570 (tt0) cc_final: 0.9240 (pp30) REVERT: N 96 ARG cc_start: 0.9576 (mtp180) cc_final: 0.9286 (tpp80) REVERT: N 102 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8381 (tp30) REVERT: N 110 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8853 (mm-30) REVERT: L 37 LEU cc_start: 0.9875 (mm) cc_final: 0.9670 (mm) REVERT: L 49 LEU cc_start: 0.9648 (mm) cc_final: 0.9305 (mm) REVERT: L 51 TYR cc_start: 0.9046 (m-10) cc_final: 0.8788 (m-80) REVERT: L 84 MET cc_start: 0.9485 (mmm) cc_final: 0.9050 (mmp) REVERT: L 98 TYR cc_start: 0.8846 (m-10) cc_final: 0.8161 (m-80) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1443 time to fit residues: 69.0775 Evaluate side-chains 253 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 12 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.041093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.027611 restraints weight = 172094.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.028965 restraints weight = 82260.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.029873 restraints weight = 48918.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.030437 restraints weight = 33305.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.030876 restraints weight = 25204.677| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 19120 Z= 0.219 Angle : 0.645 10.726 27114 Z= 0.365 Chirality : 0.042 0.244 3080 Planarity : 0.004 0.053 2419 Dihedral : 29.698 174.315 4880 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1523 helix: 1.38 (0.21), residues: 586 sheet: -2.01 (0.26), residues: 318 loop : -1.80 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 92 TYR 0.022 0.001 TYR H 51 PHE 0.027 0.002 PHE B 222 TRP 0.017 0.002 TRP A 279 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00476 (19118) covalent geometry : angle 0.64453 (27114) hydrogen bonds : bond 0.07218 ( 982) hydrogen bonds : angle 4.54776 ( 2479) metal coordination : bond 0.00205 ( 1) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.527 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: A 134 MET cc_start: 0.9252 (ttp) cc_final: 0.8945 (tmm) REVERT: A 242 MET cc_start: 0.9507 (ttm) cc_final: 0.9194 (ttp) REVERT: A 265 TYR cc_start: 0.9330 (m-80) cc_final: 0.9037 (m-80) REVERT: A 277 TYR cc_start: 0.9045 (m-80) cc_final: 0.8689 (m-80) REVERT: B 241 TRP cc_start: 0.8079 (m-10) cc_final: 0.7488 (m100) REVERT: C 3884 MET cc_start: 0.2692 (ppp) cc_final: 0.1884 (ttm) REVERT: G 50 GLU cc_start: 0.9538 (tp30) cc_final: 0.9288 (tp30) REVERT: G 60 LEU cc_start: 0.8838 (mm) cc_final: 0.8363 (mm) REVERT: G 62 ILE cc_start: 0.9770 (mt) cc_final: 0.9536 (mm) REVERT: G 84 PHE cc_start: 0.9213 (m-80) cc_final: 0.8722 (m-10) REVERT: G 90 MET cc_start: 0.9623 (mmp) cc_final: 0.9291 (mmm) REVERT: G 97 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8720 (mt-10) REVERT: G 120 MET cc_start: 0.9482 (mmp) cc_final: 0.9200 (mmt) REVERT: G 124 ILE cc_start: 0.9877 (tp) cc_final: 0.9408 (tp) REVERT: G 125 GLN cc_start: 0.9753 (mt0) cc_final: 0.9428 (mm110) REVERT: H 34 ILE cc_start: 0.9825 (mt) cc_final: 0.9563 (tp) REVERT: H 52 GLU cc_start: 0.9042 (pm20) cc_final: 0.8406 (pm20) REVERT: H 53 GLU cc_start: 0.9685 (mm-30) cc_final: 0.9274 (mm-30) REVERT: H 59 LYS cc_start: 0.9425 (tttt) cc_final: 0.9168 (tttm) REVERT: H 60 VAL cc_start: 0.9817 (t) cc_final: 0.9575 (p) REVERT: H 64 ASN cc_start: 0.9423 (m-40) cc_final: 0.9218 (m-40) REVERT: H 72 TYR cc_start: 0.9280 (m-80) cc_final: 0.8966 (m-80) REVERT: H 84 MET cc_start: 0.9154 (mmm) cc_final: 0.8715 (mmm) REVERT: H 88 TYR cc_start: 0.9481 (m-10) cc_final: 0.8867 (m-80) REVERT: I 41 GLU cc_start: 0.9358 (tt0) cc_final: 0.8784 (tm-30) REVERT: I 56 GLU cc_start: 0.9417 (tt0) cc_final: 0.8876 (mt-10) REVERT: I 64 GLU cc_start: 0.9617 (tt0) cc_final: 0.8991 (tp30) REVERT: I 83 LEU cc_start: 0.9728 (mp) cc_final: 0.9491 (pp) REVERT: I 95 LYS cc_start: 0.9641 (tptt) cc_final: 0.9359 (tppt) REVERT: J 65 ASP cc_start: 0.9246 (t70) cc_final: 0.8952 (t0) REVERT: J 76 ARG cc_start: 0.9597 (ttm110) cc_final: 0.9188 (ttm110) REVERT: J 96 ARG cc_start: 0.9475 (mtp180) cc_final: 0.9259 (mmm-85) REVERT: J 102 GLU cc_start: 0.9202 (tp30) cc_final: 0.8922 (tm-30) REVERT: J 103 LEU cc_start: 0.9611 (mt) cc_final: 0.9320 (mt) REVERT: K 41 TYR cc_start: 0.9082 (m-80) cc_final: 0.8751 (m-80) REVERT: K 50 GLU cc_start: 0.9163 (tp30) cc_final: 0.8233 (tp30) REVERT: K 54 TYR cc_start: 0.9113 (m-10) cc_final: 0.7783 (m-10) REVERT: K 80 THR cc_start: 0.9536 (p) cc_final: 0.9066 (t) REVERT: K 93 GLN cc_start: 0.9327 (tm-30) cc_final: 0.8550 (tm-30) REVERT: K 97 GLU cc_start: 0.9391 (tt0) cc_final: 0.8890 (tt0) REVERT: K 106 ASP cc_start: 0.8878 (p0) cc_final: 0.8131 (p0) REVERT: K 115 LYS cc_start: 0.9808 (mmmt) cc_final: 0.9505 (mmmm) REVERT: K 123 ASP cc_start: 0.8561 (t70) cc_final: 0.7901 (t70) REVERT: M 38 ASN cc_start: 0.9483 (m110) cc_final: 0.9098 (p0) REVERT: M 64 GLU cc_start: 0.9254 (pp20) cc_final: 0.9013 (pp20) REVERT: M 92 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8429 (mt-10) REVERT: M 94 ASN cc_start: 0.9782 (t0) cc_final: 0.9415 (m-40) REVERT: M 112 GLN cc_start: 0.9462 (mm-40) cc_final: 0.9218 (mm110) REVERT: N 30 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7687 (mtt180) REVERT: N 65 ASP cc_start: 0.9381 (t0) cc_final: 0.8859 (t0) REVERT: N 92 GLN cc_start: 0.9576 (tt0) cc_final: 0.9250 (pp30) REVERT: N 96 ARG cc_start: 0.9593 (mtp180) cc_final: 0.9282 (tpp80) REVERT: N 103 LEU cc_start: 0.9873 (mt) cc_final: 0.9602 (mt) REVERT: N 110 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8905 (mm-30) REVERT: L 49 LEU cc_start: 0.9615 (mm) cc_final: 0.8522 (tp) REVERT: L 63 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9173 (pp20) REVERT: L 68 ASP cc_start: 0.9464 (m-30) cc_final: 0.9154 (t0) REVERT: L 84 MET cc_start: 0.9498 (mmm) cc_final: 0.9051 (mmp) REVERT: L 91 LYS cc_start: 0.9729 (tttt) cc_final: 0.9283 (mtmm) REVERT: L 93 GLN cc_start: 0.9576 (tm-30) cc_final: 0.9315 (tm-30) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.1296 time to fit residues: 58.7735 Evaluate side-chains 234 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 164 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.039817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.026589 restraints weight = 172374.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027874 restraints weight = 84811.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.028738 restraints weight = 51639.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029250 restraints weight = 35885.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.029693 restraints weight = 27583.123| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 19120 Z= 0.303 Angle : 0.692 12.622 27114 Z= 0.390 Chirality : 0.043 0.228 3080 Planarity : 0.005 0.053 2419 Dihedral : 29.760 173.720 4880 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.21), residues: 1523 helix: 1.12 (0.21), residues: 585 sheet: -1.89 (0.26), residues: 308 loop : -1.76 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 92 TYR 0.017 0.002 TYR H 51 PHE 0.025 0.002 PHE H 61 TRP 0.021 0.002 TRP B 114 HIS 0.010 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00656 (19118) covalent geometry : angle 0.69187 (27114) hydrogen bonds : bond 0.08477 ( 982) hydrogen bonds : angle 4.81281 ( 2479) metal coordination : bond 0.00218 ( 1) Misc. bond : bond 0.00106 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.535 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: A 134 MET cc_start: 0.9266 (ttp) cc_final: 0.8899 (tmm) REVERT: A 242 MET cc_start: 0.9490 (ttm) cc_final: 0.9176 (ttp) REVERT: A 265 TYR cc_start: 0.9404 (m-80) cc_final: 0.9107 (m-80) REVERT: A 277 TYR cc_start: 0.8805 (m-80) cc_final: 0.8359 (m-80) REVERT: B 241 TRP cc_start: 0.8227 (m-10) cc_final: 0.7662 (m100) REVERT: C 3884 MET cc_start: 0.2558 (ppp) cc_final: 0.1678 (ttm) REVERT: G 50 GLU cc_start: 0.9544 (tp30) cc_final: 0.9290 (tp30) REVERT: G 60 LEU cc_start: 0.8827 (mm) cc_final: 0.8299 (mm) REVERT: G 70 LEU cc_start: 0.9713 (tp) cc_final: 0.9463 (tp) REVERT: G 84 PHE cc_start: 0.9202 (m-80) cc_final: 0.8682 (m-10) REVERT: G 90 MET cc_start: 0.9659 (mmp) cc_final: 0.9286 (mmm) REVERT: G 97 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8735 (mt-10) REVERT: G 112 ILE cc_start: 0.9702 (mt) cc_final: 0.9502 (mt) REVERT: G 124 ILE cc_start: 0.9900 (tp) cc_final: 0.9575 (tp) REVERT: G 125 GLN cc_start: 0.9756 (mt0) cc_final: 0.9426 (mm110) REVERT: H 29 ILE cc_start: 0.9497 (mp) cc_final: 0.9269 (mp) REVERT: H 34 ILE cc_start: 0.9848 (mt) cc_final: 0.9567 (tp) REVERT: H 49 LEU cc_start: 0.9528 (mt) cc_final: 0.8992 (mt) REVERT: H 52 GLU cc_start: 0.9061 (pm20) cc_final: 0.8444 (pm20) REVERT: H 53 GLU cc_start: 0.9667 (mm-30) cc_final: 0.9271 (mm-30) REVERT: H 68 ASP cc_start: 0.9419 (m-30) cc_final: 0.9212 (m-30) REVERT: H 84 MET cc_start: 0.9207 (mmm) cc_final: 0.8761 (mmm) REVERT: H 85 ASP cc_start: 0.9158 (m-30) cc_final: 0.8950 (m-30) REVERT: H 88 TYR cc_start: 0.9499 (m-10) cc_final: 0.8863 (m-80) REVERT: I 41 GLU cc_start: 0.9391 (tt0) cc_final: 0.8796 (tm-30) REVERT: I 56 GLU cc_start: 0.9423 (tt0) cc_final: 0.8948 (mt-10) REVERT: I 64 GLU cc_start: 0.9579 (tt0) cc_final: 0.9341 (pt0) REVERT: I 83 LEU cc_start: 0.9722 (mp) cc_final: 0.9440 (mt) REVERT: I 95 LYS cc_start: 0.9640 (tptt) cc_final: 0.9379 (tppt) REVERT: I 112 GLN cc_start: 0.9555 (mp10) cc_final: 0.9321 (mp10) REVERT: J 76 ARG cc_start: 0.9607 (ttm110) cc_final: 0.9269 (ttm110) REVERT: J 92 GLN cc_start: 0.9717 (pt0) cc_final: 0.9329 (pp30) REVERT: J 96 ARG cc_start: 0.9503 (mtp180) cc_final: 0.9272 (mmm-85) REVERT: J 102 GLU cc_start: 0.9181 (tp30) cc_final: 0.8896 (tm-30) REVERT: J 103 LEU cc_start: 0.9612 (mt) cc_final: 0.9293 (mt) REVERT: K 41 TYR cc_start: 0.9095 (m-80) cc_final: 0.8663 (m-80) REVERT: K 50 GLU cc_start: 0.9156 (tp30) cc_final: 0.8323 (tp30) REVERT: K 54 TYR cc_start: 0.9148 (m-10) cc_final: 0.8015 (m-10) REVERT: K 71 VAL cc_start: 0.9774 (t) cc_final: 0.9556 (t) REVERT: K 80 THR cc_start: 0.9573 (p) cc_final: 0.9096 (t) REVERT: K 81 ASP cc_start: 0.8849 (m-30) cc_final: 0.8620 (m-30) REVERT: K 93 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8778 (tm-30) REVERT: K 97 GLU cc_start: 0.9288 (tt0) cc_final: 0.8879 (tt0) REVERT: K 115 LYS cc_start: 0.9812 (mmmt) cc_final: 0.9496 (mmmm) REVERT: K 123 ASP cc_start: 0.8579 (t70) cc_final: 0.7965 (t70) REVERT: M 38 ASN cc_start: 0.9507 (m110) cc_final: 0.9126 (p0) REVERT: M 94 ASN cc_start: 0.9779 (t0) cc_final: 0.9417 (m-40) REVERT: M 112 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9153 (mm110) REVERT: N 30 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7605 (mtt180) REVERT: N 56 MET cc_start: 0.9493 (mmp) cc_final: 0.9268 (mmm) REVERT: N 65 ASP cc_start: 0.9402 (t0) cc_final: 0.9003 (t0) REVERT: N 92 GLN cc_start: 0.9598 (tt0) cc_final: 0.9347 (tm-30) REVERT: N 110 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8956 (mm-30) REVERT: L 49 LEU cc_start: 0.9527 (mm) cc_final: 0.9251 (mm) REVERT: L 68 ASP cc_start: 0.9479 (m-30) cc_final: 0.9160 (t0) REVERT: L 84 MET cc_start: 0.9495 (mmm) cc_final: 0.9087 (mmp) REVERT: L 93 GLN cc_start: 0.9652 (tm-30) cc_final: 0.9368 (tm-30) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1256 time to fit residues: 54.4213 Evaluate side-chains 225 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.040530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027202 restraints weight = 172177.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028532 restraints weight = 83839.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029414 restraints weight = 50460.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.029941 restraints weight = 34759.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.030403 restraints weight = 26548.939| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 19120 Z= 0.227 Angle : 0.652 11.169 27114 Z= 0.368 Chirality : 0.042 0.239 3080 Planarity : 0.004 0.045 2419 Dihedral : 29.761 174.841 4880 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1523 helix: 1.26 (0.21), residues: 586 sheet: -1.84 (0.27), residues: 316 loop : -1.71 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 76 TYR 0.013 0.001 TYR I 50 PHE 0.019 0.002 PHE H 61 TRP 0.019 0.002 TRP B 114 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00493 (19118) covalent geometry : angle 0.65161 (27114) hydrogen bonds : bond 0.07058 ( 982) hydrogen bonds : angle 4.54639 ( 2479) metal coordination : bond 0.00188 ( 1) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.446 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: A 134 MET cc_start: 0.9376 (ttp) cc_final: 0.8957 (tmm) REVERT: A 242 MET cc_start: 0.9502 (ttm) cc_final: 0.9183 (ttp) REVERT: A 265 TYR cc_start: 0.9418 (m-80) cc_final: 0.9132 (m-80) REVERT: A 277 TYR cc_start: 0.8895 (m-80) cc_final: 0.8447 (m-80) REVERT: B 241 TRP cc_start: 0.8198 (m-10) cc_final: 0.7647 (m100) REVERT: C 3884 MET cc_start: 0.2631 (ppp) cc_final: 0.1789 (ttm) REVERT: G 50 GLU cc_start: 0.9525 (tp30) cc_final: 0.9298 (tp30) REVERT: G 60 LEU cc_start: 0.8766 (mm) cc_final: 0.8434 (mm) REVERT: G 70 LEU cc_start: 0.9712 (tp) cc_final: 0.9466 (tp) REVERT: G 90 MET cc_start: 0.9626 (mmp) cc_final: 0.9263 (mmm) REVERT: G 97 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8792 (mm-30) REVERT: G 106 ASP cc_start: 0.9526 (p0) cc_final: 0.9318 (p0) REVERT: G 120 MET cc_start: 0.9491 (mmp) cc_final: 0.9110 (mmt) REVERT: G 125 GLN cc_start: 0.9750 (mt0) cc_final: 0.9412 (mm110) REVERT: H 49 LEU cc_start: 0.9565 (mt) cc_final: 0.9143 (mt) REVERT: H 52 GLU cc_start: 0.9021 (pm20) cc_final: 0.8469 (pm20) REVERT: H 53 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9211 (mm-30) REVERT: H 84 MET cc_start: 0.9159 (mmm) cc_final: 0.8684 (mmm) REVERT: H 88 TYR cc_start: 0.9464 (m-10) cc_final: 0.8802 (m-80) REVERT: H 93 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8930 (tm-30) REVERT: I 41 GLU cc_start: 0.9390 (tt0) cc_final: 0.8770 (tm-30) REVERT: I 56 GLU cc_start: 0.9393 (tt0) cc_final: 0.8795 (mt-10) REVERT: I 64 GLU cc_start: 0.9556 (tt0) cc_final: 0.9349 (pt0) REVERT: I 83 LEU cc_start: 0.9672 (mp) cc_final: 0.9331 (mt) REVERT: I 95 LYS cc_start: 0.9628 (tptt) cc_final: 0.9366 (tppt) REVERT: J 59 MET cc_start: 0.9707 (mmp) cc_final: 0.9462 (mmp) REVERT: J 76 ARG cc_start: 0.9606 (ttm110) cc_final: 0.9241 (ttm110) REVERT: J 96 ARG cc_start: 0.9415 (mtp180) cc_final: 0.9186 (mmm-85) REVERT: J 102 GLU cc_start: 0.9147 (tp30) cc_final: 0.8866 (tm-30) REVERT: J 103 LEU cc_start: 0.9604 (mt) cc_final: 0.9309 (mt) REVERT: K 41 TYR cc_start: 0.9061 (m-80) cc_final: 0.8682 (m-80) REVERT: K 50 GLU cc_start: 0.9174 (tp30) cc_final: 0.8507 (tp30) REVERT: K 54 TYR cc_start: 0.9091 (m-10) cc_final: 0.8071 (m-10) REVERT: K 80 THR cc_start: 0.9582 (p) cc_final: 0.9105 (t) REVERT: K 81 ASP cc_start: 0.8812 (m-30) cc_final: 0.8525 (m-30) REVERT: K 93 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8346 (tm-30) REVERT: K 97 GLU cc_start: 0.9235 (tt0) cc_final: 0.8468 (tt0) REVERT: K 115 LYS cc_start: 0.9815 (mmmt) cc_final: 0.9472 (mmmm) REVERT: K 123 ASP cc_start: 0.8618 (t70) cc_final: 0.7842 (t70) REVERT: M 38 ASN cc_start: 0.9476 (m110) cc_final: 0.9097 (p0) REVERT: M 64 GLU cc_start: 0.9271 (pp20) cc_final: 0.9030 (pp20) REVERT: M 94 ASN cc_start: 0.9773 (t0) cc_final: 0.9385 (m-40) REVERT: M 112 GLN cc_start: 0.9495 (mm-40) cc_final: 0.9190 (mm110) REVERT: N 30 ARG cc_start: 0.8129 (mtt90) cc_final: 0.7707 (mtt180) REVERT: N 56 MET cc_start: 0.9477 (mmp) cc_final: 0.9248 (mmm) REVERT: N 92 GLN cc_start: 0.9646 (tt0) cc_final: 0.9360 (tm-30) REVERT: N 110 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8826 (mm-30) REVERT: L 49 LEU cc_start: 0.9565 (mm) cc_final: 0.8775 (tp) REVERT: L 93 GLN cc_start: 0.9652 (tm-30) cc_final: 0.9349 (tm-30) REVERT: L 97 LEU cc_start: 0.9622 (tp) cc_final: 0.8864 (tp) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.1328 time to fit residues: 58.8343 Evaluate side-chains 233 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 58 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3822 HIS ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028812 restraints weight = 164312.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030186 restraints weight = 79186.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031120 restraints weight = 47648.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.031681 restraints weight = 32585.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032149 restraints weight = 24794.969| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19120 Z= 0.159 Angle : 0.632 10.305 27114 Z= 0.354 Chirality : 0.042 0.282 3080 Planarity : 0.004 0.050 2419 Dihedral : 29.535 177.239 4880 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1523 helix: 1.35 (0.21), residues: 588 sheet: -1.60 (0.27), residues: 318 loop : -1.58 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 76 TYR 0.015 0.001 TYR B 131 PHE 0.024 0.002 PHE G 67 TRP 0.021 0.002 TRP A 279 HIS 0.012 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00349 (19118) covalent geometry : angle 0.63219 (27114) hydrogen bonds : bond 0.06175 ( 982) hydrogen bonds : angle 4.24985 ( 2479) metal coordination : bond 0.00083 ( 1) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.464 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: A 134 MET cc_start: 0.9207 (ttp) cc_final: 0.8820 (tmm) REVERT: A 242 MET cc_start: 0.9524 (ttm) cc_final: 0.9261 (ttm) REVERT: A 265 TYR cc_start: 0.9413 (m-80) cc_final: 0.9165 (m-80) REVERT: A 277 TYR cc_start: 0.8875 (m-80) cc_final: 0.8263 (m-80) REVERT: B 241 TRP cc_start: 0.8133 (m-10) cc_final: 0.7561 (m100) REVERT: C 3884 MET cc_start: 0.3024 (ppp) cc_final: 0.2161 (ttm) REVERT: C 3935 TYR cc_start: 0.9327 (m-10) cc_final: 0.8989 (t80) REVERT: G 50 GLU cc_start: 0.9506 (tp30) cc_final: 0.9261 (tp30) REVERT: G 60 LEU cc_start: 0.8827 (mm) cc_final: 0.8285 (mm) REVERT: G 61 LEU cc_start: 0.9536 (mm) cc_final: 0.9328 (mm) REVERT: G 62 ILE cc_start: 0.9608 (mm) cc_final: 0.9119 (mm) REVERT: G 70 LEU cc_start: 0.9736 (tp) cc_final: 0.9503 (tp) REVERT: G 84 PHE cc_start: 0.9072 (m-10) cc_final: 0.8509 (m-80) REVERT: G 90 MET cc_start: 0.9598 (mmp) cc_final: 0.9161 (mmm) REVERT: G 97 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8486 (mt-10) REVERT: G 118 THR cc_start: 0.9081 (m) cc_final: 0.8797 (m) REVERT: G 120 MET cc_start: 0.9499 (mmp) cc_final: 0.9144 (mmt) REVERT: G 124 ILE cc_start: 0.9885 (tp) cc_final: 0.9423 (tp) REVERT: G 125 GLN cc_start: 0.9737 (mt0) cc_final: 0.9474 (mm110) REVERT: H 52 GLU cc_start: 0.9024 (pm20) cc_final: 0.8446 (pm20) REVERT: H 53 GLU cc_start: 0.9644 (mm-30) cc_final: 0.9154 (mm-30) REVERT: H 84 MET cc_start: 0.9190 (mmm) cc_final: 0.8783 (mmm) REVERT: H 85 ASP cc_start: 0.9118 (m-30) cc_final: 0.8917 (m-30) REVERT: H 88 TYR cc_start: 0.9411 (m-10) cc_final: 0.8734 (m-80) REVERT: H 93 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8889 (tm-30) REVERT: I 41 GLU cc_start: 0.9398 (tt0) cc_final: 0.8815 (tm-30) REVERT: I 56 GLU cc_start: 0.9369 (tt0) cc_final: 0.8823 (mt-10) REVERT: I 64 GLU cc_start: 0.9560 (tt0) cc_final: 0.9310 (pt0) REVERT: I 73 ASN cc_start: 0.9528 (t0) cc_final: 0.9068 (t0) REVERT: I 75 LYS cc_start: 0.9711 (mmtt) cc_final: 0.9444 (mmtp) REVERT: I 83 LEU cc_start: 0.9691 (mp) cc_final: 0.9295 (mt) REVERT: I 95 LYS cc_start: 0.9580 (tptt) cc_final: 0.9303 (tppt) REVERT: J 59 MET cc_start: 0.9691 (mmp) cc_final: 0.9367 (mmm) REVERT: J 76 ARG cc_start: 0.9591 (ttm110) cc_final: 0.9233 (ttm110) REVERT: J 92 GLN cc_start: 0.9662 (pt0) cc_final: 0.9328 (pp30) REVERT: J 96 ARG cc_start: 0.9346 (mtp180) cc_final: 0.9122 (mmm-85) REVERT: J 102 GLU cc_start: 0.9126 (tp30) cc_final: 0.8861 (tm-30) REVERT: J 103 LEU cc_start: 0.9582 (mt) cc_final: 0.9287 (mt) REVERT: K 41 TYR cc_start: 0.9145 (m-80) cc_final: 0.8583 (m-80) REVERT: K 50 GLU cc_start: 0.9192 (tp30) cc_final: 0.8728 (tp30) REVERT: K 54 TYR cc_start: 0.9069 (m-10) cc_final: 0.8238 (m-10) REVERT: K 70 LEU cc_start: 0.9815 (tt) cc_final: 0.9485 (tt) REVERT: K 71 VAL cc_start: 0.9766 (t) cc_final: 0.9524 (t) REVERT: K 73 GLU cc_start: 0.8765 (tt0) cc_final: 0.8542 (pt0) REVERT: K 80 THR cc_start: 0.9569 (p) cc_final: 0.9164 (t) REVERT: K 81 ASP cc_start: 0.8802 (m-30) cc_final: 0.8546 (m-30) REVERT: K 93 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8397 (tm-30) REVERT: K 97 GLU cc_start: 0.9250 (tt0) cc_final: 0.8648 (tt0) REVERT: K 110 CYS cc_start: 0.9332 (t) cc_final: 0.9069 (t) REVERT: K 115 LYS cc_start: 0.9816 (mmmt) cc_final: 0.9511 (mmmm) REVERT: K 120 MET cc_start: 0.8929 (ttm) cc_final: 0.8534 (mtp) REVERT: K 123 ASP cc_start: 0.8643 (t70) cc_final: 0.7852 (t70) REVERT: M 38 ASN cc_start: 0.9419 (m110) cc_final: 0.9082 (p0) REVERT: M 64 GLU cc_start: 0.9244 (pp20) cc_final: 0.8906 (pp20) REVERT: M 94 ASN cc_start: 0.9776 (t0) cc_final: 0.9432 (m-40) REVERT: M 112 GLN cc_start: 0.9523 (mm-40) cc_final: 0.9311 (mm110) REVERT: N 30 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7698 (mtt-85) REVERT: N 59 MET cc_start: 0.9654 (tpt) cc_final: 0.9423 (tpp) REVERT: N 92 GLN cc_start: 0.9612 (tt0) cc_final: 0.9335 (tm-30) REVERT: N 103 LEU cc_start: 0.9852 (mt) cc_final: 0.9646 (mt) REVERT: N 110 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8818 (mm-30) REVERT: L 45 ARG cc_start: 0.9127 (ttt-90) cc_final: 0.8797 (tpt170) REVERT: L 59 LYS cc_start: 0.9638 (ttmm) cc_final: 0.9403 (mmmm) REVERT: L 63 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9194 (pp20) REVERT: L 67 ARG cc_start: 0.9302 (ttp-110) cc_final: 0.8707 (ttp80) REVERT: L 68 ASP cc_start: 0.9414 (m-30) cc_final: 0.9086 (m-30) REVERT: L 84 MET cc_start: 0.9465 (mmm) cc_final: 0.9160 (mmp) REVERT: L 87 VAL cc_start: 0.9908 (t) cc_final: 0.9636 (t) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.1314 time to fit residues: 61.5646 Evaluate side-chains 244 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 40 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.041126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.027863 restraints weight = 169380.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029222 restraints weight = 82014.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030131 restraints weight = 49125.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.030725 restraints weight = 33594.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.031130 restraints weight = 25420.780| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 19120 Z= 0.220 Angle : 0.650 11.160 27114 Z= 0.367 Chirality : 0.042 0.352 3080 Planarity : 0.004 0.045 2419 Dihedral : 29.443 176.613 4880 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1523 helix: 1.31 (0.21), residues: 582 sheet: -1.50 (0.28), residues: 319 loop : -1.58 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 154 TYR 0.015 0.001 TYR L 51 PHE 0.026 0.002 PHE G 67 TRP 0.019 0.002 TRP A 279 HIS 0.008 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00480 (19118) covalent geometry : angle 0.65048 (27114) hydrogen bonds : bond 0.07024 ( 982) hydrogen bonds : angle 4.41500 ( 2479) metal coordination : bond 0.00129 ( 1) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 134 MET cc_start: 0.9160 (ttp) cc_final: 0.8832 (tmm) REVERT: A 242 MET cc_start: 0.9541 (ttm) cc_final: 0.9216 (ttp) REVERT: A 265 TYR cc_start: 0.9412 (m-80) cc_final: 0.9147 (m-80) REVERT: A 277 TYR cc_start: 0.8880 (m-80) cc_final: 0.8286 (m-80) REVERT: B 241 TRP cc_start: 0.8142 (m-10) cc_final: 0.7499 (m100) REVERT: C 3884 MET cc_start: 0.2800 (ppp) cc_final: 0.1961 (ttm) REVERT: C 3935 TYR cc_start: 0.9312 (m-10) cc_final: 0.8974 (t80) REVERT: G 50 GLU cc_start: 0.9493 (tp30) cc_final: 0.9266 (tp30) REVERT: G 60 LEU cc_start: 0.8653 (mm) cc_final: 0.8178 (mm) REVERT: G 70 LEU cc_start: 0.9745 (tp) cc_final: 0.9484 (tp) REVERT: G 84 PHE cc_start: 0.9212 (m-10) cc_final: 0.8544 (m-80) REVERT: G 90 MET cc_start: 0.9630 (mmp) cc_final: 0.9250 (mmm) REVERT: G 106 ASP cc_start: 0.9588 (p0) cc_final: 0.9348 (p0) REVERT: G 120 MET cc_start: 0.9527 (mmp) cc_final: 0.9147 (mmt) REVERT: G 124 ILE cc_start: 0.9887 (tp) cc_final: 0.9409 (tp) REVERT: G 125 GLN cc_start: 0.9743 (mt0) cc_final: 0.9410 (mm110) REVERT: H 34 ILE cc_start: 0.9820 (mt) cc_final: 0.9474 (tp) REVERT: H 49 LEU cc_start: 0.9485 (mt) cc_final: 0.9198 (mt) REVERT: H 52 GLU cc_start: 0.9031 (pm20) cc_final: 0.8476 (pm20) REVERT: H 53 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9149 (mm-30) REVERT: H 84 MET cc_start: 0.9174 (mmm) cc_final: 0.8764 (mmm) REVERT: H 85 ASP cc_start: 0.9091 (m-30) cc_final: 0.8883 (m-30) REVERT: H 88 TYR cc_start: 0.9431 (m-10) cc_final: 0.8780 (m-80) REVERT: H 90 LEU cc_start: 0.9517 (mm) cc_final: 0.9311 (mm) REVERT: I 41 GLU cc_start: 0.9381 (tt0) cc_final: 0.8789 (tm-30) REVERT: I 56 GLU cc_start: 0.9396 (tt0) cc_final: 0.9006 (mt-10) REVERT: I 64 GLU cc_start: 0.9565 (tt0) cc_final: 0.9307 (pt0) REVERT: I 73 ASN cc_start: 0.9519 (t0) cc_final: 0.9003 (t0) REVERT: I 75 LYS cc_start: 0.9706 (mmtt) cc_final: 0.9422 (mmtp) REVERT: I 83 LEU cc_start: 0.9703 (mp) cc_final: 0.9327 (mt) REVERT: I 95 LYS cc_start: 0.9600 (tptt) cc_final: 0.9336 (tppt) REVERT: J 59 MET cc_start: 0.9689 (mmp) cc_final: 0.9367 (mmm) REVERT: J 65 ASP cc_start: 0.9123 (t70) cc_final: 0.8844 (t0) REVERT: J 76 ARG cc_start: 0.9605 (ttm110) cc_final: 0.9259 (ttm110) REVERT: J 102 GLU cc_start: 0.9134 (tp30) cc_final: 0.8867 (tm-30) REVERT: J 103 LEU cc_start: 0.9609 (mt) cc_final: 0.9304 (mt) REVERT: K 41 TYR cc_start: 0.9223 (m-80) cc_final: 0.8694 (m-80) REVERT: K 50 GLU cc_start: 0.9204 (tp30) cc_final: 0.8616 (tp30) REVERT: K 54 TYR cc_start: 0.9090 (m-10) cc_final: 0.8187 (m-10) REVERT: K 80 THR cc_start: 0.9582 (p) cc_final: 0.9079 (t) REVERT: K 81 ASP cc_start: 0.8846 (m-30) cc_final: 0.8458 (m-30) REVERT: K 93 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8175 (tm-30) REVERT: K 97 GLU cc_start: 0.9168 (tt0) cc_final: 0.8561 (tt0) REVERT: K 115 LYS cc_start: 0.9809 (mmmt) cc_final: 0.9453 (mmmm) REVERT: K 120 MET cc_start: 0.9111 (ttm) cc_final: 0.8664 (mtp) REVERT: K 123 ASP cc_start: 0.8617 (t70) cc_final: 0.7741 (t70) REVERT: M 38 ASN cc_start: 0.9324 (m110) cc_final: 0.8820 (t0) REVERT: M 61 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8709 (mm-30) REVERT: M 64 GLU cc_start: 0.9286 (pp20) cc_final: 0.9086 (pp20) REVERT: M 94 ASN cc_start: 0.9801 (t0) cc_final: 0.9429 (m-40) REVERT: M 112 GLN cc_start: 0.9521 (mm-40) cc_final: 0.9316 (mm110) REVERT: N 30 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7728 (mtt180) REVERT: N 40 LYS cc_start: 0.9478 (mtmt) cc_final: 0.9259 (mtmm) REVERT: N 92 GLN cc_start: 0.9668 (tt0) cc_final: 0.9337 (tm-30) REVERT: N 110 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8884 (mm-30) REVERT: L 49 LEU cc_start: 0.9418 (mm) cc_final: 0.8782 (tp) REVERT: L 53 GLU cc_start: 0.9131 (pt0) cc_final: 0.8910 (pt0) REVERT: L 58 LEU cc_start: 0.9903 (tt) cc_final: 0.9694 (pp) REVERT: L 72 TYR cc_start: 0.9689 (m-80) cc_final: 0.9387 (m-80) REVERT: L 84 MET cc_start: 0.9454 (mmm) cc_final: 0.9123 (mmp) REVERT: L 93 GLN cc_start: 0.9691 (tm-30) cc_final: 0.9490 (tm-30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1318 time to fit residues: 56.9071 Evaluate side-chains 222 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 46 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3822 HIS ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 HIS ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.038800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.025706 restraints weight = 176384.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.026962 restraints weight = 87214.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.027792 restraints weight = 52949.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028305 restraints weight = 36733.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028689 restraints weight = 28088.177| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.162 19120 Z= 0.390 Angle : 0.762 13.483 27114 Z= 0.429 Chirality : 0.046 0.271 3080 Planarity : 0.005 0.046 2419 Dihedral : 29.718 174.464 4880 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.08 % Allowed : 1.07 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.21), residues: 1523 helix: 0.64 (0.20), residues: 585 sheet: -1.59 (0.28), residues: 316 loop : -1.66 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 92 TYR 0.020 0.002 TYR M 39 PHE 0.028 0.002 PHE G 67 TRP 0.017 0.002 TRP B 114 HIS 0.012 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00838 (19118) covalent geometry : angle 0.76180 (27114) hydrogen bonds : bond 0.09774 ( 982) hydrogen bonds : angle 5.03327 ( 2479) metal coordination : bond 0.00130 ( 1) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.034 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: A 134 MET cc_start: 0.9254 (ttp) cc_final: 0.8889 (tmm) REVERT: A 242 MET cc_start: 0.9424 (ttm) cc_final: 0.9064 (ttp) REVERT: A 265 TYR cc_start: 0.9433 (m-80) cc_final: 0.9166 (m-80) REVERT: A 277 TYR cc_start: 0.8900 (m-80) cc_final: 0.8330 (m-80) REVERT: B 241 TRP cc_start: 0.8285 (m-10) cc_final: 0.7680 (m100) REVERT: C 3854 MET cc_start: 0.5727 (pmm) cc_final: 0.5471 (ptp) REVERT: C 3884 MET cc_start: 0.2312 (ppp) cc_final: 0.1471 (ttm) REVERT: C 3948 ILE cc_start: 0.3916 (mm) cc_final: 0.3663 (mm) REVERT: G 50 GLU cc_start: 0.9516 (tp30) cc_final: 0.9278 (tp30) REVERT: G 60 LEU cc_start: 0.8770 (mm) cc_final: 0.8324 (mm) REVERT: G 70 LEU cc_start: 0.9755 (tp) cc_final: 0.9520 (tp) REVERT: G 84 PHE cc_start: 0.9337 (m-10) cc_final: 0.8651 (m-80) REVERT: G 90 MET cc_start: 0.9651 (mmp) cc_final: 0.9307 (mmm) REVERT: G 106 ASP cc_start: 0.9597 (p0) cc_final: 0.9395 (p0) REVERT: G 120 MET cc_start: 0.9547 (mmp) cc_final: 0.9287 (mmm) REVERT: G 124 ILE cc_start: 0.9897 (tp) cc_final: 0.9467 (tp) REVERT: G 125 GLN cc_start: 0.9758 (mt0) cc_final: 0.9436 (mm110) REVERT: H 49 LEU cc_start: 0.9565 (mt) cc_final: 0.8970 (mt) REVERT: H 50 ILE cc_start: 0.9462 (mm) cc_final: 0.9197 (mm) REVERT: H 51 TYR cc_start: 0.8868 (m-10) cc_final: 0.8625 (m-10) REVERT: H 52 GLU cc_start: 0.9126 (pm20) cc_final: 0.8592 (pm20) REVERT: H 53 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9222 (mp0) REVERT: H 64 ASN cc_start: 0.9459 (m-40) cc_final: 0.9242 (m-40) REVERT: H 72 TYR cc_start: 0.9273 (m-80) cc_final: 0.8961 (m-80) REVERT: H 84 MET cc_start: 0.9213 (mmm) cc_final: 0.8748 (mmm) REVERT: H 85 ASP cc_start: 0.9051 (m-30) cc_final: 0.8847 (m-30) REVERT: H 88 TYR cc_start: 0.9459 (m-10) cc_final: 0.8742 (m-80) REVERT: I 41 GLU cc_start: 0.9423 (tt0) cc_final: 0.8737 (tp30) REVERT: I 56 GLU cc_start: 0.9464 (tt0) cc_final: 0.8882 (mt-10) REVERT: I 64 GLU cc_start: 0.9569 (tt0) cc_final: 0.9318 (pt0) REVERT: I 73 ASN cc_start: 0.9584 (t0) cc_final: 0.9062 (t0) REVERT: I 75 LYS cc_start: 0.9750 (mmtt) cc_final: 0.9448 (mmtp) REVERT: I 83 LEU cc_start: 0.9723 (mp) cc_final: 0.9390 (mt) REVERT: I 95 LYS cc_start: 0.9664 (tptt) cc_final: 0.9419 (tppt) REVERT: J 59 MET cc_start: 0.9734 (mmp) cc_final: 0.9445 (mmm) REVERT: J 65 ASP cc_start: 0.9170 (t70) cc_final: 0.8871 (t0) REVERT: J 76 ARG cc_start: 0.9585 (ttm110) cc_final: 0.9249 (ttm110) REVERT: J 102 GLU cc_start: 0.9168 (tp30) cc_final: 0.8926 (tm-30) REVERT: J 103 LEU cc_start: 0.9633 (mt) cc_final: 0.9258 (mt) REVERT: K 41 TYR cc_start: 0.9256 (m-80) cc_final: 0.8627 (m-80) REVERT: K 50 GLU cc_start: 0.9177 (tp30) cc_final: 0.8291 (tp30) REVERT: K 54 TYR cc_start: 0.9078 (m-10) cc_final: 0.7862 (m-10) REVERT: K 80 THR cc_start: 0.9575 (p) cc_final: 0.9080 (t) REVERT: K 81 ASP cc_start: 0.8913 (m-30) cc_final: 0.8563 (m-30) REVERT: K 90 MET cc_start: 0.9644 (mmp) cc_final: 0.9389 (mmm) REVERT: K 93 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8307 (tm-30) REVERT: K 97 GLU cc_start: 0.9419 (tt0) cc_final: 0.8765 (tt0) REVERT: K 115 LYS cc_start: 0.9812 (mmmt) cc_final: 0.9445 (mmmm) REVERT: K 120 MET cc_start: 0.9112 (ttm) cc_final: 0.8677 (mtp) REVERT: K 123 ASP cc_start: 0.8726 (t70) cc_final: 0.8013 (t70) REVERT: M 38 ASN cc_start: 0.9386 (m110) cc_final: 0.8964 (t0) REVERT: N 30 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7624 (mtt180) REVERT: N 40 LYS cc_start: 0.9444 (mtmt) cc_final: 0.9234 (mtmm) REVERT: N 92 GLN cc_start: 0.9733 (tt0) cc_final: 0.9398 (tm-30) REVERT: N 110 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8935 (mm-30) REVERT: L 43 VAL cc_start: 0.9303 (t) cc_final: 0.9015 (t) REVERT: L 59 LYS cc_start: 0.9751 (ttmm) cc_final: 0.9489 (ttmm) REVERT: L 68 ASP cc_start: 0.9452 (m-30) cc_final: 0.9224 (m-30) REVERT: L 84 MET cc_start: 0.9441 (mmm) cc_final: 0.9030 (mmt) REVERT: L 93 GLN cc_start: 0.9737 (tm-30) cc_final: 0.9485 (tm-30) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.1268 time to fit residues: 54.2303 Evaluate side-chains 215 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3822 HIS ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.040883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.027558 restraints weight = 169504.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.028859 restraints weight = 83243.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.029774 restraints weight = 50680.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.030413 restraints weight = 34709.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.030733 restraints weight = 25758.327| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19120 Z= 0.202 Angle : 0.672 11.354 27114 Z= 0.377 Chirality : 0.043 0.241 3080 Planarity : 0.004 0.047 2419 Dihedral : 29.699 175.949 4880 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1523 helix: 0.98 (0.21), residues: 583 sheet: -1.44 (0.28), residues: 309 loop : -1.62 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 76 TYR 0.021 0.001 TYR I 57 PHE 0.024 0.002 PHE G 67 TRP 0.020 0.002 TRP A 279 HIS 0.006 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00439 (19118) covalent geometry : angle 0.67206 (27114) hydrogen bonds : bond 0.06724 ( 982) hydrogen bonds : angle 4.56287 ( 2479) metal coordination : bond 0.00081 ( 1) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.522 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: A 134 MET cc_start: 0.9239 (ttp) cc_final: 0.8777 (tmm) REVERT: A 242 MET cc_start: 0.9513 (ttm) cc_final: 0.9173 (ttp) REVERT: A 265 TYR cc_start: 0.9422 (m-80) cc_final: 0.9157 (m-80) REVERT: A 277 TYR cc_start: 0.8841 (m-80) cc_final: 0.8145 (m-80) REVERT: B 241 TRP cc_start: 0.8280 (m-10) cc_final: 0.7639 (m100) REVERT: C 3884 MET cc_start: 0.2438 (ppp) cc_final: 0.1595 (ttm) REVERT: G 50 GLU cc_start: 0.9483 (tp30) cc_final: 0.9252 (tp30) REVERT: G 60 LEU cc_start: 0.8652 (mm) cc_final: 0.8298 (mm) REVERT: G 62 ILE cc_start: 0.9692 (mm) cc_final: 0.9226 (mm) REVERT: G 70 LEU cc_start: 0.9726 (tp) cc_final: 0.9491 (tp) REVERT: G 84 PHE cc_start: 0.9246 (m-10) cc_final: 0.8580 (m-80) REVERT: G 90 MET cc_start: 0.9597 (mmp) cc_final: 0.9239 (mmm) REVERT: G 97 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8532 (mm-30) REVERT: G 120 MET cc_start: 0.9553 (mmp) cc_final: 0.9313 (mmm) REVERT: H 22 LEU cc_start: 0.8707 (mm) cc_final: 0.8306 (mm) REVERT: H 25 ASN cc_start: 0.7799 (m-40) cc_final: 0.7576 (m-40) REVERT: H 26 ILE cc_start: 0.9751 (tt) cc_final: 0.9518 (tt) REVERT: H 29 ILE cc_start: 0.9536 (pt) cc_final: 0.9311 (pt) REVERT: H 34 ILE cc_start: 0.9800 (mt) cc_final: 0.9391 (tp) REVERT: H 49 LEU cc_start: 0.9558 (mt) cc_final: 0.9006 (mt) REVERT: H 50 ILE cc_start: 0.9434 (mm) cc_final: 0.9169 (mm) REVERT: H 51 TYR cc_start: 0.8867 (m-10) cc_final: 0.8640 (m-10) REVERT: H 52 GLU cc_start: 0.9041 (pm20) cc_final: 0.8504 (pm20) REVERT: H 53 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9211 (mp0) REVERT: H 58 LEU cc_start: 0.9855 (tt) cc_final: 0.9613 (pp) REVERT: H 64 ASN cc_start: 0.9453 (m-40) cc_final: 0.9242 (m-40) REVERT: H 72 TYR cc_start: 0.9221 (m-80) cc_final: 0.8875 (m-80) REVERT: H 84 MET cc_start: 0.9142 (mmm) cc_final: 0.8666 (mmm) REVERT: H 88 TYR cc_start: 0.9400 (m-10) cc_final: 0.8666 (m-80) REVERT: I 41 GLU cc_start: 0.9402 (tt0) cc_final: 0.8832 (tm-30) REVERT: I 56 GLU cc_start: 0.9367 (tt0) cc_final: 0.8799 (mt-10) REVERT: I 64 GLU cc_start: 0.9538 (tt0) cc_final: 0.9264 (pt0) REVERT: I 73 ASN cc_start: 0.9534 (t0) cc_final: 0.9019 (t0) REVERT: I 75 LYS cc_start: 0.9717 (mmtt) cc_final: 0.9429 (mmtp) REVERT: I 83 LEU cc_start: 0.9709 (mp) cc_final: 0.9295 (mt) REVERT: I 95 LYS cc_start: 0.9626 (tptt) cc_final: 0.9356 (tppt) REVERT: J 59 MET cc_start: 0.9655 (mmp) cc_final: 0.9363 (mmm) REVERT: J 65 ASP cc_start: 0.9065 (t70) cc_final: 0.8639 (t0) REVERT: J 69 ARG cc_start: 0.9287 (ttm110) cc_final: 0.8976 (ttm110) REVERT: J 76 ARG cc_start: 0.9600 (ttm110) cc_final: 0.9263 (ttm110) REVERT: J 103 LEU cc_start: 0.9522 (mt) cc_final: 0.9203 (mt) REVERT: K 41 TYR cc_start: 0.9162 (m-80) cc_final: 0.8677 (m-80) REVERT: K 50 GLU cc_start: 0.9171 (tp30) cc_final: 0.8505 (tp30) REVERT: K 54 TYR cc_start: 0.9043 (m-10) cc_final: 0.8022 (m-10) REVERT: K 80 THR cc_start: 0.9571 (p) cc_final: 0.9057 (t) REVERT: K 81 ASP cc_start: 0.8815 (m-30) cc_final: 0.8464 (m-30) REVERT: K 93 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8169 (tm-30) REVERT: K 97 GLU cc_start: 0.9385 (tt0) cc_final: 0.8625 (tt0) REVERT: K 110 CYS cc_start: 0.9145 (t) cc_final: 0.8938 (t) REVERT: K 115 LYS cc_start: 0.9824 (mmmt) cc_final: 0.9443 (mmmm) REVERT: K 120 MET cc_start: 0.9015 (ttm) cc_final: 0.8571 (mtp) REVERT: K 123 ASP cc_start: 0.8597 (t70) cc_final: 0.7747 (t70) REVERT: M 38 ASN cc_start: 0.9292 (m110) cc_final: 0.8888 (t0) REVERT: M 64 GLU cc_start: 0.9254 (pp20) cc_final: 0.9012 (pp20) REVERT: M 94 ASN cc_start: 0.9783 (t0) cc_final: 0.9420 (m-40) REVERT: N 65 ASP cc_start: 0.9404 (t70) cc_final: 0.9062 (t0) REVERT: N 92 GLN cc_start: 0.9688 (tt0) cc_final: 0.9364 (tm-30) REVERT: N 110 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8835 (mm-30) REVERT: L 30 THR cc_start: 0.9547 (p) cc_final: 0.9293 (t) REVERT: L 43 VAL cc_start: 0.9240 (t) cc_final: 0.9036 (t) REVERT: L 59 LYS cc_start: 0.9705 (ttmm) cc_final: 0.9476 (ttmm) REVERT: L 72 TYR cc_start: 0.9698 (m-80) cc_final: 0.9347 (m-80) REVERT: L 84 MET cc_start: 0.9431 (mmm) cc_final: 0.8959 (mmt) REVERT: L 93 GLN cc_start: 0.9717 (tm-30) cc_final: 0.9510 (tm-30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1310 time to fit residues: 57.3423 Evaluate side-chains 226 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 0.3980 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 44 optimal weight: 40.0000 chunk 55 optimal weight: 6.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3822 HIS ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.039266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.026136 restraints weight = 177462.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.027409 restraints weight = 87286.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.028249 restraints weight = 52616.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.028766 restraints weight = 36304.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029178 restraints weight = 27825.528| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 19120 Z= 0.318 Angle : 0.725 12.469 27114 Z= 0.407 Chirality : 0.044 0.248 3080 Planarity : 0.005 0.045 2419 Dihedral : 29.696 174.883 4880 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1523 helix: 0.71 (0.21), residues: 583 sheet: -1.50 (0.28), residues: 309 loop : -1.68 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 76 TYR 0.019 0.002 TYR I 57 PHE 0.026 0.002 PHE G 67 TRP 0.016 0.002 TRP B 114 HIS 0.007 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00688 (19118) covalent geometry : angle 0.72527 (27114) hydrogen bonds : bond 0.08519 ( 982) hydrogen bonds : angle 4.87080 ( 2479) metal coordination : bond 0.00108 ( 1) Misc. bond : bond 0.00016 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3046 Ramachandran restraints generated. 1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.513 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: A 134 MET cc_start: 0.9177 (ttp) cc_final: 0.8740 (tmm) REVERT: A 242 MET cc_start: 0.9451 (ttm) cc_final: 0.9077 (ttp) REVERT: A 265 TYR cc_start: 0.9436 (m-80) cc_final: 0.9164 (m-80) REVERT: A 277 TYR cc_start: 0.8900 (m-80) cc_final: 0.8317 (m-80) REVERT: C 3884 MET cc_start: 0.2490 (ppp) cc_final: 0.1622 (ttm) REVERT: G 50 GLU cc_start: 0.9490 (tp30) cc_final: 0.9263 (tp30) REVERT: G 60 LEU cc_start: 0.8685 (mm) cc_final: 0.8271 (mm) REVERT: G 84 PHE cc_start: 0.9320 (m-10) cc_final: 0.8658 (m-80) REVERT: G 90 MET cc_start: 0.9625 (mmp) cc_final: 0.9272 (mmm) REVERT: G 120 MET cc_start: 0.9540 (mmp) cc_final: 0.9279 (mmm) REVERT: H 49 LEU cc_start: 0.9565 (mt) cc_final: 0.8992 (mt) REVERT: H 50 ILE cc_start: 0.9448 (mm) cc_final: 0.9180 (mm) REVERT: H 51 TYR cc_start: 0.8916 (m-10) cc_final: 0.8642 (m-10) REVERT: H 52 GLU cc_start: 0.9069 (pm20) cc_final: 0.8571 (pm20) REVERT: H 53 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9236 (mp0) REVERT: H 64 ASN cc_start: 0.9440 (m-40) cc_final: 0.9231 (m-40) REVERT: H 84 MET cc_start: 0.9138 (mmm) cc_final: 0.8692 (mmm) REVERT: H 85 ASP cc_start: 0.9064 (m-30) cc_final: 0.8856 (m-30) REVERT: H 88 TYR cc_start: 0.9450 (m-10) cc_final: 0.8726 (m-80) REVERT: I 56 GLU cc_start: 0.9445 (tt0) cc_final: 0.8864 (mt-10) REVERT: I 64 GLU cc_start: 0.9557 (tt0) cc_final: 0.9294 (pt0) REVERT: I 73 ASN cc_start: 0.9549 (t0) cc_final: 0.9010 (t0) REVERT: I 75 LYS cc_start: 0.9751 (mmtt) cc_final: 0.9436 (mmtp) REVERT: I 83 LEU cc_start: 0.9734 (mp) cc_final: 0.9388 (mt) REVERT: I 95 LYS cc_start: 0.9660 (tptt) cc_final: 0.9407 (tppt) REVERT: J 59 MET cc_start: 0.9673 (mmp) cc_final: 0.9410 (mmm) REVERT: J 65 ASP cc_start: 0.9122 (t70) cc_final: 0.8715 (t0) REVERT: J 69 ARG cc_start: 0.9313 (ttm110) cc_final: 0.8995 (ttm110) REVERT: J 76 ARG cc_start: 0.9595 (ttm110) cc_final: 0.9241 (ttm110) REVERT: K 41 TYR cc_start: 0.9191 (m-80) cc_final: 0.8687 (m-80) REVERT: K 50 GLU cc_start: 0.9176 (tp30) cc_final: 0.8310 (tp30) REVERT: K 54 TYR cc_start: 0.9075 (m-10) cc_final: 0.7860 (m-10) REVERT: K 80 THR cc_start: 0.9556 (p) cc_final: 0.9047 (t) REVERT: K 81 ASP cc_start: 0.8868 (m-30) cc_final: 0.8507 (m-30) REVERT: K 90 MET cc_start: 0.9614 (mmp) cc_final: 0.9407 (mmm) REVERT: K 93 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8388 (tm-30) REVERT: K 97 GLU cc_start: 0.9374 (tt0) cc_final: 0.8713 (tt0) REVERT: K 110 CYS cc_start: 0.9142 (t) cc_final: 0.8932 (t) REVERT: K 115 LYS cc_start: 0.9818 (mmmt) cc_final: 0.9455 (mmmm) REVERT: K 120 MET cc_start: 0.9091 (ttm) cc_final: 0.8652 (mtp) REVERT: K 123 ASP cc_start: 0.8589 (t70) cc_final: 0.7867 (t70) REVERT: K 125 GLN cc_start: 0.9356 (mp10) cc_final: 0.9115 (mp10) REVERT: M 36 LYS cc_start: 0.9269 (mttm) cc_final: 0.9063 (mmtm) REVERT: M 38 ASN cc_start: 0.9314 (m110) cc_final: 0.8953 (t0) REVERT: M 64 GLU cc_start: 0.9280 (pp20) cc_final: 0.9068 (pp20) REVERT: M 94 ASN cc_start: 0.9799 (t0) cc_final: 0.9454 (m-40) REVERT: N 65 ASP cc_start: 0.9436 (t70) cc_final: 0.9232 (t0) REVERT: N 92 GLN cc_start: 0.9722 (tt0) cc_final: 0.9374 (tm-30) REVERT: N 110 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8945 (mm-30) REVERT: L 43 VAL cc_start: 0.9310 (t) cc_final: 0.9041 (t) REVERT: L 58 LEU cc_start: 0.9927 (tt) cc_final: 0.9707 (pp) REVERT: L 84 MET cc_start: 0.9412 (mmm) cc_final: 0.8833 (mmt) REVERT: L 85 ASP cc_start: 0.9528 (m-30) cc_final: 0.8674 (t70) REVERT: L 91 LYS cc_start: 0.9404 (ptpt) cc_final: 0.9148 (pttm) REVERT: L 93 GLN cc_start: 0.9748 (tm-30) cc_final: 0.9521 (tm-30) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1199 time to fit residues: 50.2357 Evaluate side-chains 214 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 135 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3822 HIS ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.039589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.026468 restraints weight = 176634.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.027758 restraints weight = 86381.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028616 restraints weight = 51980.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029182 restraints weight = 35813.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029538 restraints weight = 27155.216| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 19120 Z= 0.281 Angle : 0.709 12.424 27114 Z= 0.399 Chirality : 0.043 0.232 3080 Planarity : 0.004 0.046 2419 Dihedral : 29.798 175.208 4880 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.21), residues: 1523 helix: 0.73 (0.21), residues: 583 sheet: -1.52 (0.28), residues: 310 loop : -1.63 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 76 TYR 0.019 0.002 TYR L 51 PHE 0.035 0.002 PHE K 67 TRP 0.017 0.002 TRP A 279 HIS 0.007 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00607 (19118) covalent geometry : angle 0.70941 (27114) hydrogen bonds : bond 0.07756 ( 982) hydrogen bonds : angle 4.79603 ( 2479) metal coordination : bond 0.00087 ( 1) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.33 seconds wall clock time: 57 minutes 37.08 seconds (3457.08 seconds total)