Starting phenix.real_space_refine on Mon Sep 14 13:45:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pww_20513/09_2026/6pww_20513.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pww_20513/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6pww_20513/09_2026/6pww_20513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pww_20513/09_2026/6pww_20513.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pww_20513/09_2026/6pww_20513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pww_20513/09_2026/6pww_20513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pww_20513/09_2026/6pww_20513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pww_20513/09_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-2.2.1-6174/lib/python3.11/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: 3.94, per 1000 atoms: 0.22 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: 1.51 Conformation dependent library (CDL) restraints added in 556.3 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: 2.11 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: 3.86 Time building geometry restraints manager: 2.00 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=" C3' DG O 94 " pdb=" C2' DG O 94 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DG O 85 " pdb=" C2' DG O 85 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT P 51 " pdb=" C2' DT P 51 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT O 35 " pdb=" C2' DT O 35 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.49e+00 bond pdb=" C3' DC O 51 " pdb=" C2' DC O 51 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.23e+00 ... (remaining 19113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 26903 2.76 - 5.51: 201 5.51 - 8.27: 4 8.27 - 11.03: 4 11.03 - 13.78: 2 Bond angle restraints: 27114 Sorted by residual: angle pdb=" O4' DA P 14 " pdb=" C4' DA P 14 " pdb=" C3' DA P 14 " ideal model delta sigma weight residual 106.00 102.17 3.83 6.00e-01 2.78e+00 4.07e+01 angle pdb=" O4' DG P 130 " pdb=" C4' DG P 130 " pdb=" C3' DG P 130 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.41e+01 angle pdb=" O4' DC O 79 " pdb=" C1' DC O 79 " pdb=" N1 DC O 79 " ideal model delta sigma weight residual 108.00 111.41 -3.41 7.00e-01 2.04e+00 2.37e+01 angle pdb=" N3 DT O 46 " pdb=" C4 DT O 46 " pdb=" O4 DT O 46 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 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 ... (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: 1964 0.038 - 0.076: 780 0.076 - 0.114: 275 0.114 - 0.152: 58 0.152 - 0.190: 3 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' DG P 94 " pdb=" C4' DG P 94 " pdb=" O3' DG P 94 " pdb=" C2' DG P 94 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C3' DC P 126 " pdb=" C4' DC P 126 " pdb=" O3' DC P 126 " pdb=" C2' DC P 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.07e-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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.120 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.007 0.584 19120 Z= 0.477 Angle : 0.756 13.783 27114 Z= 0.613 Chirality : 0.046 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/Z covalent geometry : bond 0.00506 / 0.46 (19118) covalent geometry : angle 0.75613 / 0.61 (27114) hydrogen bonds : bond 0.14153 / 9.19 ( 982) hydrogen bonds : angle 5.79919 / 3.97 ( 2479) metal coordination : bond 0.58448 / 30.76 ( 1) Misc. bond : bond 0.00006 / 0.00 ( 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 : 0.717 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: 0.8999 (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: 0.7353 (m-10) REVERT: C 3969 ASN cc_start: 0.6113 (m-40) cc_final: 0.5891 (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: 0.7972 (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: 0.8499 (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: 0.8384 (m-80) REVERT: I 41 GLU cc_start: 0.9319 (tt0) cc_final: 0.8815 (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: 0.9306 (pp) REVERT: I 64 GLU cc_start: 0.9633 (tt0) cc_final: 0.9334 (mm-30) 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: 0.9482 (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: 0.8822 (m-80) REVERT: K 50 GLU cc_start: 0.9060 (tp30) cc_final: 0.8667 (tp30) REVERT: K 61 LEU cc_start: 0.9489 (mm) cc_final: 0.9158 (mp) REVERT: K 65 LEU cc_start: 0.9768 (mm) cc_final: 0.9478 (mt) 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: 0.9202 (mt) REVERT: K 97 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8471 (mt-10) REVERT: K 106 ASP cc_start: 0.8629 (p0) cc_final: 0.8351 (p0) REVERT: K 119 ILE cc_start: 0.8920 (pt) cc_final: 0.8693 (tp) REVERT: K 122 LYS cc_start: 0.9028 (pttp) cc_final: 0.8786 (ptmm) REVERT: K 123 ASP cc_start: 0.8800 (t70) cc_final: 0.8148 (t70) REVERT: M 36 LYS cc_start: 0.9235 (mttm) cc_final: 0.8822 (mtmm) REVERT: M 56 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9168 (mt-10) REVERT: M 90 ASP cc_start: 0.9615 (t0) cc_final: 0.9382 (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: 0.8047 (mtt-85) 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: 0.8701 (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: 0.9021 (tp) REVERT: L 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8365 (m-80) outliers start: 16 outliers final: 4 residues processed: 370 average time/residue: 0.1672 time to fit residues: 89.5755 Evaluate side-chains 265 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 258 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 250 ASN A 285 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN B 178 HIS B 265 ASN B 289 GLN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN C3906 ASN G 39 HIS G 68 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** 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 106 HIS K 108 ASN K 113 HIS ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 64 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027749 restraints weight = 169769.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029087 restraints weight = 80610.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029970 restraints weight = 48037.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.030509 restraints weight = 32832.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030940 restraints weight = 24885.314| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19120 Z= 0.191 Angle : 0.744 10.515 27114 Z= 0.415 Chirality : 0.050 0.341 3080 Planarity : 0.006 0.063 2419 Dihedral : 30.165 171.758 4880 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % 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: -1.54 (0.21), residues: 1523 helix: 0.74 (0.21), residues: 586 sheet: -2.23 (0.26), residues: 309 loop : -2.04 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C3821 TYR 0.020 0.002 TYR C3874 PHE 0.026 0.002 PHE K 67 TRP 0.031 0.002 TRP B 156 HIS 0.013 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.19 (19118) covalent geometry : angle 0.74443 / 0.42 (27114) hydrogen bonds : bond 0.08025 / 5.36 ( 982) hydrogen bonds : angle 4.88513 / 3.34 ( 2479) metal coordination : bond 0.00612 / 0.32 ( 1) Misc. bond : bond 0.00012 / 0.01 ( 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 320 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.587 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: 0.9376 (ttp) cc_final: 0.9010 (tmm) REVERT: A 242 MET cc_start: 0.9468 (ttm) cc_final: 0.9159 (ttp) REVERT: A 265 TYR cc_start: 0.9289 (m-80) cc_final: 0.9037 (m-80) REVERT: A 277 TYR cc_start: 0.8914 (m-10) cc_final: 0.8680 (m-80) REVERT: C 3872 GLU cc_start: 0.5231 (mt-10) cc_final: 0.5021 (mt-10) REVERT: G 50 GLU cc_start: 0.9576 (tp30) cc_final: 0.9288 (tp30) REVERT: G 60 LEU cc_start: 0.8871 (mm) cc_final: 0.8625 (mm) REVERT: G 61 LEU cc_start: 0.9354 (mm) cc_final: 0.9101 (mm) REVERT: G 62 ILE cc_start: 0.9791 (mt) cc_final: 0.9561 (mm) REVERT: G 65 LEU cc_start: 0.9818 (mm) cc_final: 0.9478 (mm) REVERT: G 70 LEU cc_start: 0.9673 (tp) cc_final: 0.9204 (tp) REVERT: G 84 PHE cc_start: 0.9252 (m-80) cc_final: 0.9021 (m-10) REVERT: G 90 MET cc_start: 0.9623 (mmp) cc_final: 0.9303 (mmm) REVERT: G 97 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8839 (mt-10) REVERT: G 108 ASN cc_start: 0.9411 (t0) cc_final: 0.9165 (t0) REVERT: G 109 LEU cc_start: 0.9852 (tt) cc_final: 0.9650 (pp) REVERT: G 118 THR cc_start: 0.9002 (m) cc_final: 0.8707 (m) REVERT: G 125 GLN cc_start: 0.9722 (mt0) cc_final: 0.9421 (mm110) REVERT: G 130 ILE cc_start: 0.9743 (mm) cc_final: 0.9537 (mm) REVERT: G 133 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7696 (pt0) REVERT: H 25 ASN cc_start: 0.8318 (m-40) cc_final: 0.7653 (t0) REVERT: H 85 ASP cc_start: 0.9090 (m-30) cc_final: 0.8865 (m-30) REVERT: H 88 TYR cc_start: 0.9450 (m-10) cc_final: 0.8980 (m-80) REVERT: H 93 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8652 (tm-30) REVERT: I 41 GLU cc_start: 0.9355 (tt0) cc_final: 0.8795 (tm-30) REVERT: I 56 GLU cc_start: 0.9414 (tt0) cc_final: 0.8960 (mt-10) REVERT: I 64 GLU cc_start: 0.9636 (tt0) cc_final: 0.9030 (tp30) REVERT: I 83 LEU cc_start: 0.9714 (mp) cc_final: 0.9466 (pp) REVERT: I 95 LYS cc_start: 0.9639 (tptt) cc_final: 0.9336 (tppt) REVERT: J 59 MET cc_start: 0.9697 (mmm) cc_final: 0.9436 (mmm) REVERT: J 62 PHE cc_start: 0.9689 (t80) cc_final: 0.9401 (t80) REVERT: J 65 ASP cc_start: 0.9241 (t70) cc_final: 0.8919 (t0) REVERT: J 76 ARG cc_start: 0.9579 (ttm110) cc_final: 0.9111 (ttm110) REVERT: J 91 ILE cc_start: 0.9848 (mp) cc_final: 0.9584 (tt) REVERT: J 92 GLN cc_start: 0.9701 (pt0) cc_final: 0.9300 (pp30) REVERT: J 96 ARG cc_start: 0.9486 (mtp180) cc_final: 0.9249 (mmm-85) REVERT: J 102 GLU cc_start: 0.9189 (tp30) cc_final: 0.8905 (tm-30) REVERT: J 103 LEU cc_start: 0.9653 (mt) cc_final: 0.9290 (mt) REVERT: K 41 TYR cc_start: 0.8988 (m-80) cc_final: 0.8735 (m-80) REVERT: K 50 GLU cc_start: 0.9097 (tp30) cc_final: 0.8517 (tp30) REVERT: K 61 LEU cc_start: 0.9471 (mm) cc_final: 0.9158 (mp) REVERT: K 80 THR cc_start: 0.9549 (p) cc_final: 0.9185 (p) REVERT: K 89 VAL cc_start: 0.9778 (p) cc_final: 0.9407 (m) REVERT: K 90 MET cc_start: 0.9537 (mmp) cc_final: 0.9272 (mmt) REVERT: K 115 LYS cc_start: 0.9784 (mmmt) cc_final: 0.9487 (mmmm) REVERT: K 118 THR cc_start: 0.9157 (p) cc_final: 0.8871 (m) REVERT: K 123 ASP cc_start: 0.8294 (t70) cc_final: 0.7412 (t70) REVERT: K 124 ILE cc_start: 0.9795 (mp) cc_final: 0.9571 (tp) REVERT: K 125 GLN cc_start: 0.9459 (mt0) cc_final: 0.9055 (mm110) REVERT: M 38 ASN cc_start: 0.9472 (m110) cc_final: 0.9071 (p0) REVERT: M 56 GLU cc_start: 0.9492 (mt-10) cc_final: 0.9237 (mt-10) REVERT: M 73 ASN cc_start: 0.9443 (t0) cc_final: 0.9115 (t0) REVERT: M 94 ASN cc_start: 0.9751 (t0) cc_final: 0.9366 (m-40) REVERT: M 112 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9130 (mm110) REVERT: N 30 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7962 (mtt-85) REVERT: N 64 ASN cc_start: 0.9832 (m-40) cc_final: 0.9624 (m-40) REVERT: N 65 ASP cc_start: 0.9353 (t0) cc_final: 0.8852 (t0) REVERT: N 92 GLN cc_start: 0.9581 (tt0) cc_final: 0.9246 (pp30) REVERT: N 96 ARG cc_start: 0.9600 (mtp180) cc_final: 0.9319 (tpp80) REVERT: N 97 LEU cc_start: 0.9693 (mm) cc_final: 0.9416 (mm) REVERT: N 110 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8882 (mm-30) REVERT: L 37 LEU cc_start: 0.9877 (mm) cc_final: 0.9636 (mm) REVERT: L 45 ARG cc_start: 0.9391 (ttt-90) cc_final: 0.9119 (ttp80) REVERT: L 51 TYR cc_start: 0.9072 (m-10) cc_final: 0.8574 (m-80) REVERT: L 53 GLU cc_start: 0.9474 (tt0) cc_final: 0.8708 (tt0) REVERT: L 72 TYR cc_start: 0.9711 (m-80) cc_final: 0.9255 (m-10) REVERT: L 84 MET cc_start: 0.9479 (mmm) cc_final: 0.8956 (mmt) REVERT: L 91 LYS cc_start: 0.9764 (tttt) cc_final: 0.9384 (mtpt) REVERT: L 98 TYR cc_start: 0.8988 (m-10) cc_final: 0.8319 (m-80) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.1512 time to fit residues: 72.0437 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 : 0.447 ------------------------------------------------------------------------------- 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: 0.0010 chunk 171 optimal weight: 0.7980 chunk 157 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 137 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 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** N 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.041574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.027964 restraints weight = 168963.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.029339 restraints weight = 80204.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.030251 restraints weight = 47215.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030843 restraints weight = 31886.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.031262 restraints weight = 23726.544| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19120 Z= 0.173 Angle : 0.704 10.026 27114 Z= 0.395 Chirality : 0.049 0.359 3080 Planarity : 0.005 0.050 2419 Dihedral : 30.059 172.099 4880 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.08 % Allowed : 4.51 % 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: -1.20 (0.21), residues: 1523 helix: 1.11 (0.21), residues: 587 sheet: -2.09 (0.26), residues: 309 loop : -1.94 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C3871 TYR 0.026 0.002 TYR H 51 PHE 0.048 0.002 PHE B 222 TRP 0.019 0.002 TRP B 156 HIS 0.007 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (19118) covalent geometry : angle 0.70435 / 0.40 (27114) hydrogen bonds : bond 0.07505 / 5.02 ( 982) hydrogen bonds : angle 4.65650 / 3.18 ( 2479) metal coordination : bond 0.00367 / 0.19 ( 1) Misc. bond : bond 0.00052 / 0.03 ( 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 309 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.438 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: A 134 MET cc_start: 0.9259 (ttp) cc_final: 0.8950 (tmm) REVERT: A 242 MET cc_start: 0.9493 (ttm) cc_final: 0.9193 (ttp) REVERT: A 265 TYR cc_start: 0.9297 (m-80) cc_final: 0.9055 (m-80) REVERT: A 277 TYR cc_start: 0.8943 (m-10) cc_final: 0.8696 (m-10) REVERT: B 241 TRP cc_start: 0.8284 (m-10) cc_final: 0.7573 (m100) REVERT: G 50 GLU cc_start: 0.9565 (tp30) cc_final: 0.9298 (tp30) REVERT: G 61 LEU cc_start: 0.9412 (mm) cc_final: 0.9091 (mm) REVERT: G 62 ILE cc_start: 0.9784 (mt) cc_final: 0.9462 (mm) REVERT: G 70 LEU cc_start: 0.9667 (tp) cc_final: 0.9151 (tp) REVERT: G 84 PHE cc_start: 0.9225 (m-80) cc_final: 0.8988 (m-10) REVERT: G 90 MET cc_start: 0.9637 (mmp) cc_final: 0.9273 (mmm) REVERT: G 93 GLN cc_start: 0.9591 (tm-30) cc_final: 0.8365 (tp40) REVERT: G 97 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8437 (mt-10) REVERT: G 124 ILE cc_start: 0.9863 (tp) cc_final: 0.9392 (tp) REVERT: G 125 GLN cc_start: 0.9730 (mt0) cc_final: 0.9458 (mm110) REVERT: H 25 ASN cc_start: 0.8032 (m-40) cc_final: 0.7487 (t0) REVERT: H 26 ILE cc_start: 0.9704 (tt) cc_final: 0.9494 (tt) REVERT: H 34 ILE cc_start: 0.9798 (mt) cc_final: 0.9549 (tp) REVERT: H 60 VAL cc_start: 0.9831 (t) cc_final: 0.9520 (t) REVERT: H 72 TYR cc_start: 0.9309 (m-80) cc_final: 0.8955 (m-80) REVERT: H 85 ASP cc_start: 0.9110 (m-30) cc_final: 0.8908 (m-30) REVERT: H 88 TYR cc_start: 0.9448 (m-10) cc_final: 0.9137 (m-80) REVERT: H 93 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8627 (tm-30) REVERT: I 41 GLU cc_start: 0.9367 (tt0) cc_final: 0.8784 (tm-30) REVERT: I 56 GLU cc_start: 0.9456 (tt0) cc_final: 0.8951 (mt-10) REVERT: I 64 GLU cc_start: 0.9606 (tt0) cc_final: 0.9338 (pt0) REVERT: I 83 LEU cc_start: 0.9722 (mp) cc_final: 0.9488 (pp) REVERT: I 95 LYS cc_start: 0.9637 (tptt) cc_final: 0.9377 (tppt) REVERT: J 56 MET cc_start: 0.9284 (tpp) cc_final: 0.9070 (tpp) REVERT: J 59 MET cc_start: 0.9695 (mmm) cc_final: 0.9452 (mmm) REVERT: J 68 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8807 (tm-30) REVERT: J 76 ARG cc_start: 0.9603 (ttm110) cc_final: 0.9112 (ttm110) REVERT: J 91 ILE cc_start: 0.9830 (mp) cc_final: 0.9586 (tt) REVERT: J 92 GLN cc_start: 0.9683 (pt0) cc_final: 0.9296 (pp30) REVERT: J 96 ARG cc_start: 0.9390 (mtp180) cc_final: 0.9161 (mmm-85) REVERT: J 102 GLU cc_start: 0.9203 (tp30) cc_final: 0.8920 (tm-30) REVERT: J 103 LEU cc_start: 0.9599 (mt) cc_final: 0.9347 (mt) REVERT: K 41 TYR cc_start: 0.9017 (m-80) cc_final: 0.8736 (m-80) REVERT: K 50 GLU cc_start: 0.9120 (tp30) cc_final: 0.8583 (tp30) REVERT: K 61 LEU cc_start: 0.9474 (mm) cc_final: 0.9173 (mp) REVERT: K 62 ILE cc_start: 0.9630 (mm) cc_final: 0.9394 (mm) REVERT: K 80 THR cc_start: 0.9522 (p) cc_final: 0.9221 (p) REVERT: K 89 VAL cc_start: 0.9805 (p) cc_final: 0.9387 (m) REVERT: K 93 GLN cc_start: 0.9415 (tm-30) cc_final: 0.8551 (tm-30) REVERT: K 106 ASP cc_start: 0.8898 (p0) cc_final: 0.8640 (p0) REVERT: K 110 CYS cc_start: 0.9256 (t) cc_final: 0.8941 (t) REVERT: K 115 LYS cc_start: 0.9791 (mmmt) cc_final: 0.9482 (mmmm) REVERT: K 120 MET cc_start: 0.8786 (mtp) cc_final: 0.8570 (mtp) REVERT: K 123 ASP cc_start: 0.8087 (t70) cc_final: 0.7316 (t70) REVERT: K 124 ILE cc_start: 0.9751 (mp) cc_final: 0.9550 (tp) REVERT: K 125 GLN cc_start: 0.9488 (mt0) cc_final: 0.9062 (mm110) REVERT: M 38 ASN cc_start: 0.9484 (m110) cc_final: 0.9070 (p0) REVERT: M 56 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9232 (mt-10) REVERT: M 64 GLU cc_start: 0.9290 (pp20) cc_final: 0.9041 (pp20) REVERT: M 94 ASN cc_start: 0.9759 (t0) cc_final: 0.9369 (m-40) REVERT: M 112 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9217 (mm110) REVERT: N 30 ARG cc_start: 0.8213 (mtt90) cc_final: 0.7934 (mtt-85) REVERT: N 59 MET cc_start: 0.9743 (mmt) cc_final: 0.9492 (mmt) REVERT: N 64 ASN cc_start: 0.9842 (m-40) cc_final: 0.9634 (m-40) REVERT: N 65 ASP cc_start: 0.9362 (t0) cc_final: 0.8862 (t0) REVERT: N 92 GLN cc_start: 0.9542 (tt0) cc_final: 0.9307 (pp30) REVERT: N 105 LYS cc_start: 0.9679 (mttt) cc_final: 0.9317 (mmmt) REVERT: N 110 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8891 (mm-30) REVERT: L 44 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8802 (ttmm) REVERT: L 53 GLU cc_start: 0.9563 (tt0) cc_final: 0.8782 (tt0) REVERT: L 68 ASP cc_start: 0.9144 (t70) cc_final: 0.8535 (t0) REVERT: L 72 TYR cc_start: 0.9519 (m-80) cc_final: 0.9221 (m-10) REVERT: L 74 GLU cc_start: 0.9386 (tm-30) cc_final: 0.9071 (tm-30) REVERT: L 84 MET cc_start: 0.9481 (mmm) cc_final: 0.9065 (mmp) REVERT: L 93 GLN cc_start: 0.9598 (tm-30) cc_final: 0.9386 (tm-30) outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.1337 time to fit residues: 63.0416 Evaluate side-chains 252 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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: 20.0000 chunk 73 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS B 310 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** 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** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.026421 restraints weight = 177279.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.027705 restraints weight = 85033.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028561 restraints weight = 50672.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029107 restraints weight = 34585.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.029442 restraints weight = 26127.487| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 19120 Z= 0.290 Angle : 0.785 12.304 27114 Z= 0.436 Chirality : 0.050 0.321 3080 Planarity : 0.005 0.057 2419 Dihedral : 30.062 170.771 4880 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -1.28 (0.21), residues: 1523 helix: 0.91 (0.20), residues: 585 sheet: -1.82 (0.28), residues: 304 loop : -2.02 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 294 TYR 0.022 0.002 TYR H 51 PHE 0.026 0.003 PHE B 222 TRP 0.035 0.003 TRP B 114 HIS 0.017 0.002 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.29 (19118) covalent geometry : angle 0.78533 / 0.44 (27114) hydrogen bonds : bond 0.09864 / 6.62 ( 982) hydrogen bonds : angle 5.04257 / 3.46 ( 2479) metal coordination : bond 0.00248 / 0.13 ( 1) Misc. bond : bond 0.00083 / 0.04 ( 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 282 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.607 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: 0.9299 (ttp) cc_final: 0.8914 (tmm) REVERT: A 242 MET cc_start: 0.9489 (ttm) cc_final: 0.9161 (ttp) REVERT: A 265 TYR cc_start: 0.9379 (m-80) cc_final: 0.9071 (m-80) REVERT: B 241 TRP cc_start: 0.8280 (m-10) cc_final: 0.7688 (m100) REVERT: C 3884 MET cc_start: 0.3144 (ppp) cc_final: 0.2299 (ttm) REVERT: G 50 GLU cc_start: 0.9521 (tp30) cc_final: 0.9259 (tp30) REVERT: G 60 LEU cc_start: 0.8731 (mm) cc_final: 0.8297 (mm) REVERT: G 62 ILE cc_start: 0.9779 (mt) cc_final: 0.9553 (mm) REVERT: G 70 LEU cc_start: 0.9656 (tp) cc_final: 0.9125 (tp) REVERT: G 84 PHE cc_start: 0.9217 (m-80) cc_final: 0.8996 (m-10) REVERT: G 90 MET cc_start: 0.9641 (mmp) cc_final: 0.9262 (mmm) REVERT: G 97 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8600 (mt-10) REVERT: G 106 ASP cc_start: 0.9568 (p0) cc_final: 0.9353 (p0) REVERT: G 124 ILE cc_start: 0.9882 (tp) cc_final: 0.9470 (tp) REVERT: G 125 GLN cc_start: 0.9738 (mt0) cc_final: 0.9412 (mm110) REVERT: H 25 ASN cc_start: 0.8126 (m-40) cc_final: 0.7464 (t0) REVERT: H 26 ILE cc_start: 0.9732 (tt) cc_final: 0.9488 (tt) REVERT: H 34 ILE cc_start: 0.9846 (mt) cc_final: 0.9584 (tp) REVERT: H 72 TYR cc_start: 0.9362 (m-80) cc_final: 0.9069 (m-80) REVERT: H 84 MET cc_start: 0.9244 (mmm) cc_final: 0.8673 (mmm) REVERT: H 88 TYR cc_start: 0.9491 (m-10) cc_final: 0.8955 (m-80) REVERT: H 93 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8698 (tm-30) REVERT: I 41 GLU cc_start: 0.9374 (tt0) cc_final: 0.8719 (tp30) REVERT: I 56 GLU cc_start: 0.9470 (tt0) cc_final: 0.8866 (mt-10) REVERT: I 64 GLU cc_start: 0.9623 (tt0) cc_final: 0.9326 (mt-10) REVERT: I 83 LEU cc_start: 0.9761 (mp) cc_final: 0.9439 (mt) REVERT: I 95 LYS cc_start: 0.9650 (tptt) cc_final: 0.9392 (tppt) REVERT: J 59 MET cc_start: 0.9723 (mmm) cc_final: 0.9484 (mmm) REVERT: J 65 ASP cc_start: 0.9348 (t70) cc_final: 0.9049 (t70) REVERT: J 68 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8829 (tm-30) REVERT: J 76 ARG cc_start: 0.9607 (ttm110) cc_final: 0.9116 (ttm110) REVERT: J 91 ILE cc_start: 0.9845 (mp) cc_final: 0.9622 (tt) REVERT: J 92 GLN cc_start: 0.9720 (pt0) cc_final: 0.9332 (pp30) REVERT: J 96 ARG cc_start: 0.9520 (mtp180) cc_final: 0.9303 (mmm-85) REVERT: J 102 GLU cc_start: 0.9187 (tp30) cc_final: 0.8912 (tm-30) REVERT: J 103 LEU cc_start: 0.9618 (mt) cc_final: 0.9338 (mt) REVERT: K 41 TYR cc_start: 0.9077 (m-80) cc_final: 0.8705 (m-80) REVERT: K 50 GLU cc_start: 0.9161 (tp30) cc_final: 0.8645 (tp30) REVERT: K 61 LEU cc_start: 0.9487 (mm) cc_final: 0.9143 (mp) REVERT: K 93 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8886 (tm-30) REVERT: K 115 LYS cc_start: 0.9787 (mmmt) cc_final: 0.9477 (mmmm) REVERT: K 123 ASP cc_start: 0.8352 (t70) cc_final: 0.7889 (t70) REVERT: K 125 GLN cc_start: 0.9619 (mt0) cc_final: 0.9214 (mm110) REVERT: M 56 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9253 (mt-10) REVERT: M 64 GLU cc_start: 0.9341 (pp20) cc_final: 0.9117 (pp20) REVERT: M 92 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8721 (mt-10) REVERT: M 94 ASN cc_start: 0.9765 (t0) cc_final: 0.9506 (t0) REVERT: M 112 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9128 (mm110) REVERT: N 30 ARG cc_start: 0.8279 (mtt90) cc_final: 0.8044 (mtt-85) REVERT: N 59 MET cc_start: 0.9705 (mmt) cc_final: 0.9457 (tpp) REVERT: N 65 ASP cc_start: 0.9378 (t0) cc_final: 0.8925 (t0) REVERT: N 92 GLN cc_start: 0.9588 (tt0) cc_final: 0.9230 (pp30) REVERT: N 102 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8176 (tp30) REVERT: N 103 LEU cc_start: 0.9861 (mt) cc_final: 0.9490 (mt) REVERT: N 110 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8944 (mm-30) REVERT: L 68 ASP cc_start: 0.9148 (t70) cc_final: 0.8546 (t0) REVERT: L 72 TYR cc_start: 0.9585 (m-80) cc_final: 0.9257 (m-10) REVERT: L 84 MET cc_start: 0.9459 (mmm) cc_final: 0.9073 (mmp) REVERT: L 93 GLN cc_start: 0.9636 (tm-30) cc_final: 0.9413 (tm-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1332 time to fit residues: 57.6258 Evaluate side-chains 227 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 20.0000 chunk 166 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN C3822 HIS ** 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** ** K 108 ASN ** 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 = 0.3091 r_free = 0.3091 target = 0.040852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.027343 restraints weight = 170737.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.028679 restraints weight = 82153.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.029567 restraints weight = 49054.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.030123 restraints weight = 33657.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030532 restraints weight = 25607.447| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 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 = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19120 Z= 0.188 Angle : 0.711 12.050 27114 Z= 0.398 Chirality : 0.049 0.366 3080 Planarity : 0.004 0.047 2419 Dihedral : 30.079 171.714 4880 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % 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: -1.07 (0.21), residues: 1523 helix: 1.15 (0.21), residues: 585 sheet: -1.74 (0.28), residues: 300 loop : -1.95 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 76 TYR 0.026 0.002 TYR H 51 PHE 0.025 0.002 PHE H 61 TRP 0.019 0.002 TRP A 279 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.19 (19118) covalent geometry : angle 0.71080 / 0.40 (27114) hydrogen bonds : bond 0.07707 / 5.17 ( 982) hydrogen bonds : angle 4.72995 / 3.24 ( 2479) metal coordination : bond 0.00270 / 0.14 ( 1) Misc. bond : bond 0.00044 / 0.02 ( 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 296 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.651 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: 0.9279 (ttp) cc_final: 0.8903 (tmm) REVERT: A 242 MET cc_start: 0.9473 (ttm) cc_final: 0.9144 (ttp) REVERT: A 265 TYR cc_start: 0.9364 (m-80) cc_final: 0.9117 (m-80) REVERT: A 277 TYR cc_start: 0.9033 (m-10) cc_final: 0.8704 (m-10) REVERT: A 291 HIS cc_start: 0.7063 (t-90) cc_final: 0.6306 (t70) REVERT: B 241 TRP cc_start: 0.8215 (m-10) cc_final: 0.7632 (m100) REVERT: C 3884 MET cc_start: 0.2681 (ppp) cc_final: 0.1882 (ttm) REVERT: G 50 GLU cc_start: 0.9558 (tp30) cc_final: 0.9272 (tp30) REVERT: G 60 LEU cc_start: 0.8732 (mm) cc_final: 0.8317 (mm) REVERT: G 61 LEU cc_start: 0.9498 (mm) cc_final: 0.9176 (mm) REVERT: G 70 LEU cc_start: 0.9668 (tp) cc_final: 0.9439 (tp) REVERT: G 84 PHE cc_start: 0.9187 (m-80) cc_final: 0.8986 (m-10) REVERT: G 90 MET cc_start: 0.9630 (mmp) cc_final: 0.9260 (mmm) REVERT: G 97 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8670 (mt-10) REVERT: G 115 LYS cc_start: 0.9710 (mtpt) cc_final: 0.9482 (mppt) REVERT: G 124 ILE cc_start: 0.9853 (tp) cc_final: 0.9484 (tp) REVERT: G 125 GLN cc_start: 0.9742 (mt0) cc_final: 0.9433 (mm110) REVERT: H 34 ILE cc_start: 0.9836 (mt) cc_final: 0.9531 (tp) REVERT: H 72 TYR cc_start: 0.9380 (m-80) cc_final: 0.9000 (m-80) REVERT: H 88 TYR cc_start: 0.9464 (m-10) cc_final: 0.9128 (m-80) REVERT: H 93 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8748 (tm-30) REVERT: I 41 GLU cc_start: 0.9365 (tt0) cc_final: 0.8806 (tm-30) REVERT: I 56 GLU cc_start: 0.9473 (tt0) cc_final: 0.8880 (mt-10) REVERT: I 64 GLU cc_start: 0.9595 (tt0) cc_final: 0.9348 (pt0) REVERT: I 83 LEU cc_start: 0.9753 (mp) cc_final: 0.9344 (mt) REVERT: I 95 LYS cc_start: 0.9629 (tptt) cc_final: 0.9367 (tppt) REVERT: I 101 THR cc_start: 0.8963 (p) cc_final: 0.8730 (p) REVERT: J 65 ASP cc_start: 0.9320 (t70) cc_final: 0.9041 (t70) REVERT: J 68 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8798 (tm-30) REVERT: J 76 ARG cc_start: 0.9607 (ttm110) cc_final: 0.9169 (ttm110) REVERT: J 91 ILE cc_start: 0.9835 (mp) cc_final: 0.9629 (tt) REVERT: J 92 GLN cc_start: 0.9711 (pt0) cc_final: 0.9324 (pp30) REVERT: J 102 GLU cc_start: 0.9206 (tp30) cc_final: 0.8926 (tm-30) REVERT: J 103 LEU cc_start: 0.9619 (mt) cc_final: 0.9308 (mt) REVERT: K 41 TYR cc_start: 0.9076 (m-80) cc_final: 0.8636 (m-80) REVERT: K 50 GLU cc_start: 0.9137 (tp30) cc_final: 0.8603 (tp30) REVERT: K 61 LEU cc_start: 0.9475 (mm) cc_final: 0.9131 (mp) REVERT: K 93 GLN cc_start: 0.9316 (tm-30) cc_final: 0.8944 (tm-30) REVERT: K 115 LYS cc_start: 0.9801 (mmmt) cc_final: 0.9481 (mmmm) REVERT: K 123 ASP cc_start: 0.8318 (t70) cc_final: 0.7539 (t70) REVERT: M 64 GLU cc_start: 0.9341 (pp20) cc_final: 0.9088 (pp20) REVERT: M 73 ASN cc_start: 0.9445 (t0) cc_final: 0.9142 (t0) REVERT: M 75 LYS cc_start: 0.9518 (mmpt) cc_final: 0.9094 (mmmm) REVERT: M 90 ASP cc_start: 0.9580 (t70) cc_final: 0.9356 (t70) REVERT: M 94 ASN cc_start: 0.9780 (t0) cc_final: 0.9502 (t0) REVERT: M 112 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9123 (mm110) REVERT: N 30 ARG cc_start: 0.8259 (mtt90) cc_final: 0.7814 (mtt-85) REVERT: N 65 ASP cc_start: 0.9381 (t0) cc_final: 0.8920 (t0) REVERT: N 92 GLN cc_start: 0.9608 (tt0) cc_final: 0.9333 (tm-30) REVERT: N 110 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8887 (mm-30) REVERT: L 74 GLU cc_start: 0.9385 (tm-30) cc_final: 0.9093 (tm-30) REVERT: L 84 MET cc_start: 0.9471 (mmm) cc_final: 0.9040 (mmp) REVERT: L 93 GLN cc_start: 0.9634 (tm-30) cc_final: 0.9378 (tm-30) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.1368 time to fit residues: 62.8357 Evaluate side-chains 240 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 20.0000 chunk 172 optimal weight: 5.9990 chunk 74 optimal weight: 40.0000 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 133 optimal weight: 0.0050 chunk 116 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS C3822 HIS 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** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.040824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.027321 restraints weight = 169948.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.028650 restraints weight = 81505.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.029531 restraints weight = 48647.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.030062 restraints weight = 33253.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030508 restraints weight = 25214.080| |-----------------------------------------------------------------------------| 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: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 19120 Z= 0.188 Angle : 0.716 11.301 27114 Z= 0.397 Chirality : 0.049 0.356 3080 Planarity : 0.004 0.050 2419 Dihedral : 30.037 172.078 4880 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.48 % 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: -1.00 (0.21), residues: 1523 helix: 1.19 (0.21), residues: 585 sheet: -1.73 (0.28), residues: 299 loop : -1.88 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 76 TYR 0.027 0.002 TYR H 51 PHE 0.025 0.002 PHE H 61 TRP 0.018 0.002 TRP A 279 HIS 0.011 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.19 (19118) covalent geometry : angle 0.71574 / 0.40 (27114) hydrogen bonds : bond 0.07756 / 5.18 ( 982) hydrogen bonds : angle 4.64071 / 3.19 ( 2479) metal coordination : bond 0.00192 / 0.10 ( 1) Misc. bond : bond 0.00062 / 0.03 ( 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 298 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.555 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: 0.9285 (ttp) cc_final: 0.8888 (tmm) REVERT: A 242 MET cc_start: 0.9487 (ttm) cc_final: 0.9160 (ttp) REVERT: A 265 TYR cc_start: 0.9355 (m-80) cc_final: 0.9127 (m-80) REVERT: A 277 TYR cc_start: 0.9024 (m-10) cc_final: 0.8770 (m-10) REVERT: A 291 HIS cc_start: 0.7122 (t70) cc_final: 0.6781 (t70) REVERT: B 241 TRP cc_start: 0.8208 (m-10) cc_final: 0.7647 (m100) REVERT: G 61 LEU cc_start: 0.9554 (mm) cc_final: 0.9172 (mm) REVERT: G 70 LEU cc_start: 0.9644 (tp) cc_final: 0.9402 (tp) REVERT: G 84 PHE cc_start: 0.9162 (m-80) cc_final: 0.8955 (m-10) REVERT: G 90 MET cc_start: 0.9629 (mmp) cc_final: 0.9225 (mmm) REVERT: G 93 GLN cc_start: 0.9592 (tm-30) cc_final: 0.8648 (tm-30) REVERT: G 124 ILE cc_start: 0.9876 (tp) cc_final: 0.9515 (tp) REVERT: G 125 GLN cc_start: 0.9748 (mt0) cc_final: 0.9455 (mm110) REVERT: H 34 ILE cc_start: 0.9825 (mt) cc_final: 0.9541 (tp) REVERT: H 52 GLU cc_start: 0.9067 (pm20) cc_final: 0.8425 (pm20) REVERT: H 53 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9290 (mm-30) REVERT: H 72 TYR cc_start: 0.9361 (m-80) cc_final: 0.9078 (m-80) REVERT: H 85 ASP cc_start: 0.9166 (m-30) cc_final: 0.8948 (m-30) REVERT: H 93 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8741 (tm-30) REVERT: I 41 GLU cc_start: 0.9367 (tt0) cc_final: 0.8805 (tm-30) REVERT: I 56 GLU cc_start: 0.9450 (tt0) cc_final: 0.8844 (mt-10) REVERT: I 64 GLU cc_start: 0.9585 (tt0) cc_final: 0.9344 (pt0) REVERT: I 83 LEU cc_start: 0.9700 (mp) cc_final: 0.9354 (mt) REVERT: I 95 LYS cc_start: 0.9619 (tptt) cc_final: 0.9354 (tppt) REVERT: J 65 ASP cc_start: 0.9288 (t70) cc_final: 0.9043 (t70) REVERT: J 76 ARG cc_start: 0.9615 (ttm110) cc_final: 0.9270 (ttm110) REVERT: J 92 GLN cc_start: 0.9694 (pt0) cc_final: 0.9354 (pp30) REVERT: J 102 GLU cc_start: 0.9158 (tp30) cc_final: 0.8900 (tm-30) REVERT: J 103 LEU cc_start: 0.9606 (mt) cc_final: 0.9328 (mt) REVERT: K 41 TYR cc_start: 0.9056 (m-80) cc_final: 0.8583 (m-80) REVERT: K 50 GLU cc_start: 0.9141 (tp30) cc_final: 0.8119 (tp30) REVERT: K 54 TYR cc_start: 0.9129 (m-10) cc_final: 0.7775 (m-10) REVERT: K 61 LEU cc_start: 0.9441 (mm) cc_final: 0.9006 (mp) REVERT: K 80 THR cc_start: 0.9572 (p) cc_final: 0.9106 (t) REVERT: K 90 MET cc_start: 0.9578 (mmp) cc_final: 0.9308 (mmm) REVERT: K 93 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8366 (tm-30) REVERT: K 110 CYS cc_start: 0.9168 (t) cc_final: 0.8965 (t) REVERT: K 115 LYS cc_start: 0.9804 (mmmt) cc_final: 0.9481 (mmmm) REVERT: K 123 ASP cc_start: 0.8403 (t70) cc_final: 0.7627 (t70) REVERT: M 64 GLU cc_start: 0.9320 (pp20) cc_final: 0.9049 (pp20) REVERT: M 90 ASP cc_start: 0.9562 (t70) cc_final: 0.9342 (t70) REVERT: M 94 ASN cc_start: 0.9790 (t0) cc_final: 0.9485 (t0) REVERT: M 112 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9218 (mm110) REVERT: N 30 ARG cc_start: 0.8253 (mtt90) cc_final: 0.7796 (mtt-85) REVERT: N 59 MET cc_start: 0.9686 (mmt) cc_final: 0.9454 (tpp) REVERT: N 92 GLN cc_start: 0.9611 (tt0) cc_final: 0.9352 (tm-30) REVERT: N 103 LEU cc_start: 0.9867 (mt) cc_final: 0.9264 (mt) REVERT: N 110 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8905 (mm-30) REVERT: L 45 ARG cc_start: 0.9396 (ttt-90) cc_final: 0.8991 (mmm-85) REVERT: L 46 ILE cc_start: 0.9423 (mp) cc_final: 0.9214 (mp) REVERT: L 68 ASP cc_start: 0.9332 (m-30) cc_final: 0.9111 (m-30) REVERT: L 74 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9105 (tm-30) REVERT: L 84 MET cc_start: 0.9470 (mmm) cc_final: 0.9018 (mmp) REVERT: L 93 GLN cc_start: 0.9656 (tm-30) cc_final: 0.9399 (tm-30) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.1351 time to fit residues: 62.2834 Evaluate side-chains 234 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 7.9990 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3822 HIS ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 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** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN N 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027786 restraints weight = 172933.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029114 restraints weight = 84085.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.029978 restraints weight = 50310.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030543 restraints weight = 34842.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030961 restraints weight = 26591.553| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 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 = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 19120 Z= 0.164 Angle : 0.694 10.859 27114 Z= 0.386 Chirality : 0.048 0.364 3080 Planarity : 0.004 0.046 2419 Dihedral : 29.984 172.767 4880 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.86 % 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: -0.86 (0.21), residues: 1523 helix: 1.29 (0.21), residues: 586 sheet: -1.65 (0.28), residues: 298 loop : -1.79 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 77 TYR 0.029 0.001 TYR H 51 PHE 0.024 0.002 PHE H 61 TRP 0.017 0.002 TRP A 279 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (19118) covalent geometry : angle 0.69420 / 0.39 (27114) hydrogen bonds : bond 0.07245 / 4.84 ( 982) hydrogen bonds : angle 4.48207 / 3.08 ( 2479) metal coordination : bond 0.00117 / 0.06 ( 1) Misc. bond : bond 0.00047 / 0.02 ( 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 294 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.558 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: 0.9268 (ttp) cc_final: 0.8881 (tmm) REVERT: A 242 MET cc_start: 0.9502 (ttm) cc_final: 0.9171 (ttp) REVERT: A 265 TYR cc_start: 0.9389 (m-80) cc_final: 0.9157 (m-80) REVERT: A 277 TYR cc_start: 0.8915 (m-10) cc_final: 0.8689 (m-10) REVERT: B 241 TRP cc_start: 0.8148 (m-10) cc_final: 0.7475 (m-10) REVERT: G 54 TYR cc_start: 0.9265 (m-10) cc_final: 0.8982 (m-10) REVERT: G 61 LEU cc_start: 0.9581 (mm) cc_final: 0.9042 (mm) REVERT: G 62 ILE cc_start: 0.9693 (mm) cc_final: 0.8716 (mm) REVERT: G 67 PHE cc_start: 0.9668 (t80) cc_final: 0.9357 (t80) REVERT: G 70 LEU cc_start: 0.9679 (tp) cc_final: 0.9436 (tp) REVERT: G 90 MET cc_start: 0.9618 (mmp) cc_final: 0.9203 (mmm) REVERT: G 93 GLN cc_start: 0.9600 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 97 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8118 (mm-30) REVERT: G 106 ASP cc_start: 0.9660 (p0) cc_final: 0.9450 (p0) REVERT: G 125 GLN cc_start: 0.9724 (mt0) cc_final: 0.9435 (mm110) REVERT: H 34 ILE cc_start: 0.9828 (mt) cc_final: 0.9514 (tp) REVERT: H 52 GLU cc_start: 0.9036 (pm20) cc_final: 0.8363 (pm20) REVERT: H 53 GLU cc_start: 0.9626 (mm-30) cc_final: 0.9267 (mm-30) REVERT: H 72 TYR cc_start: 0.9375 (m-80) cc_final: 0.9066 (m-80) REVERT: H 93 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8738 (tm-30) REVERT: I 41 GLU cc_start: 0.9356 (tt0) cc_final: 0.8738 (tm-30) REVERT: I 56 GLU cc_start: 0.9446 (tt0) cc_final: 0.8813 (mt-10) REVERT: I 64 GLU cc_start: 0.9552 (tt0) cc_final: 0.9273 (pt0) REVERT: I 83 LEU cc_start: 0.9689 (mp) cc_final: 0.9398 (mt) REVERT: I 95 LYS cc_start: 0.9589 (tptt) cc_final: 0.9312 (tppt) REVERT: J 59 MET cc_start: 0.9633 (mmp) cc_final: 0.9421 (mmp) REVERT: J 65 ASP cc_start: 0.9264 (t70) cc_final: 0.9035 (t0) REVERT: J 76 ARG cc_start: 0.9595 (ttm110) cc_final: 0.9212 (ttm110) REVERT: J 92 GLN cc_start: 0.9696 (pt0) cc_final: 0.9326 (pp30) REVERT: J 102 GLU cc_start: 0.9174 (tp30) cc_final: 0.8901 (tm-30) REVERT: J 103 LEU cc_start: 0.9587 (mt) cc_final: 0.9282 (mt) REVERT: J 105 LYS cc_start: 0.9708 (mmpt) cc_final: 0.9504 (mmmt) REVERT: K 41 TYR cc_start: 0.9032 (m-80) cc_final: 0.8554 (m-80) REVERT: K 50 GLU cc_start: 0.9156 (tp30) cc_final: 0.8222 (tp30) REVERT: K 54 TYR cc_start: 0.9100 (m-10) cc_final: 0.7769 (m-10) REVERT: K 61 LEU cc_start: 0.9440 (mm) cc_final: 0.9039 (mp) REVERT: K 80 THR cc_start: 0.9549 (p) cc_final: 0.9037 (t) REVERT: K 110 CYS cc_start: 0.9175 (t) cc_final: 0.8916 (t) REVERT: K 115 LYS cc_start: 0.9809 (mmmt) cc_final: 0.9494 (mmmm) REVERT: K 123 ASP cc_start: 0.8429 (t70) cc_final: 0.7509 (t70) REVERT: M 38 ASN cc_start: 0.9462 (m110) cc_final: 0.9127 (p0) REVERT: M 64 GLU cc_start: 0.9320 (pp20) cc_final: 0.9033 (pp20) REVERT: M 90 ASP cc_start: 0.9567 (t70) cc_final: 0.9346 (t70) REVERT: M 92 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8639 (mt-10) REVERT: M 94 ASN cc_start: 0.9776 (t0) cc_final: 0.9495 (t0) REVERT: M 112 GLN cc_start: 0.9474 (mm-40) cc_final: 0.9236 (mm110) REVERT: N 30 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7776 (mtt-85) REVERT: N 59 MET cc_start: 0.9656 (mmt) cc_final: 0.9412 (tpp) REVERT: N 92 GLN cc_start: 0.9608 (tt0) cc_final: 0.9280 (pp30) REVERT: N 110 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8910 (mm-30) REVERT: L 45 ARG cc_start: 0.9294 (ttt-90) cc_final: 0.8992 (mmm-85) REVERT: L 49 LEU cc_start: 0.9598 (mm) cc_final: 0.9123 (mm) REVERT: L 68 ASP cc_start: 0.9314 (m-30) cc_final: 0.9110 (m-30) REVERT: L 74 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9063 (tm-30) REVERT: L 84 MET cc_start: 0.9459 (mmm) cc_final: 0.9084 (mmp) REVERT: L 93 GLN cc_start: 0.9647 (tm-30) cc_final: 0.9362 (tm-30) outliers start: 1 outliers final: 1 residues processed: 293 average time/residue: 0.1207 time to fit residues: 54.8856 Evaluate side-chains 240 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 7.9990 chunk 137 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.039925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.026720 restraints weight = 171917.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027981 restraints weight = 83631.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028843 restraints weight = 50744.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.029404 restraints weight = 34945.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029823 restraints weight = 26568.979| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 19120 Z= 0.274 Angle : 0.778 12.516 27114 Z= 0.430 Chirality : 0.050 0.334 3080 Planarity : 0.005 0.049 2419 Dihedral : 29.972 171.679 4880 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.78 (0.20), residues: 585 sheet: -1.66 (0.28), residues: 303 loop : -1.79 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 76 TYR 0.026 0.002 TYR I 50 PHE 0.024 0.002 PHE H 61 TRP 0.014 0.002 TRP B 114 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.27 (19118) covalent geometry : angle 0.77771 / 0.43 (27114) hydrogen bonds : bond 0.09299 / 6.26 ( 982) hydrogen bonds : angle 4.91875 / 3.40 ( 2479) metal coordination : bond 0.00212 / 0.11 ( 1) Misc. bond : bond 0.00096 / 0.05 ( 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 269 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.587 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: 0.9239 (ttp) cc_final: 0.8857 (tmm) REVERT: A 242 MET cc_start: 0.9468 (ttm) cc_final: 0.9152 (ttp) REVERT: A 265 TYR cc_start: 0.9408 (m-80) cc_final: 0.9142 (m-80) REVERT: A 277 TYR cc_start: 0.8944 (m-10) cc_final: 0.8694 (m-10) REVERT: B 241 TRP cc_start: 0.8156 (m-10) cc_final: 0.7510 (m-10) REVERT: G 54 TYR cc_start: 0.9323 (m-10) cc_final: 0.9013 (m-10) REVERT: G 67 PHE cc_start: 0.9717 (t80) cc_final: 0.9388 (t80) REVERT: G 68 GLN cc_start: 0.9378 (pp30) cc_final: 0.9171 (pp30) REVERT: G 70 LEU cc_start: 0.9665 (tp) cc_final: 0.9419 (tp) REVERT: G 84 PHE cc_start: 0.9418 (m-10) cc_final: 0.8824 (m-80) REVERT: G 90 MET cc_start: 0.9640 (mmp) cc_final: 0.9256 (mmm) REVERT: G 93 GLN cc_start: 0.9613 (tm-30) cc_final: 0.8658 (tm-30) REVERT: G 97 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8959 (mt-10) REVERT: G 125 GLN cc_start: 0.9737 (mt0) cc_final: 0.9412 (mm-40) REVERT: H 29 ILE cc_start: 0.9504 (mp) cc_final: 0.9301 (mp) REVERT: H 34 ILE cc_start: 0.9844 (mt) cc_final: 0.9611 (tp) REVERT: H 49 LEU cc_start: 0.9437 (mt) cc_final: 0.9148 (mt) REVERT: H 52 GLU cc_start: 0.9056 (pm20) cc_final: 0.8410 (pm20) REVERT: H 53 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9250 (mm-30) REVERT: H 72 TYR cc_start: 0.9480 (m-80) cc_final: 0.9113 (m-80) REVERT: H 84 MET cc_start: 0.9213 (mmm) cc_final: 0.8742 (mmm) REVERT: H 85 ASP cc_start: 0.9120 (m-30) cc_final: 0.8898 (m-30) REVERT: H 93 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8775 (tm-30) REVERT: I 41 GLU cc_start: 0.9389 (tt0) cc_final: 0.8666 (tp30) REVERT: I 56 GLU cc_start: 0.9439 (tt0) cc_final: 0.8796 (mt-10) REVERT: I 64 GLU cc_start: 0.9579 (tt0) cc_final: 0.9333 (pt0) REVERT: I 83 LEU cc_start: 0.9692 (mp) cc_final: 0.9453 (mt) REVERT: I 95 LYS cc_start: 0.9619 (tptt) cc_final: 0.9365 (tppt) REVERT: J 65 ASP cc_start: 0.9338 (t70) cc_final: 0.9107 (t0) REVERT: J 76 ARG cc_start: 0.9622 (ttm110) cc_final: 0.9252 (ttm110) REVERT: J 92 GLN cc_start: 0.9618 (pt0) cc_final: 0.9328 (pp30) REVERT: J 102 GLU cc_start: 0.9163 (tp30) cc_final: 0.8893 (tm-30) REVERT: J 103 LEU cc_start: 0.9610 (mt) cc_final: 0.9305 (mt) REVERT: K 41 TYR cc_start: 0.9259 (m-80) cc_final: 0.8468 (m-80) REVERT: K 50 GLU cc_start: 0.9200 (tp30) cc_final: 0.8626 (tp30) REVERT: K 61 LEU cc_start: 0.9459 (mm) cc_final: 0.8889 (mp) REVERT: K 80 THR cc_start: 0.9574 (p) cc_final: 0.9081 (t) REVERT: K 81 ASP cc_start: 0.8705 (m-30) cc_final: 0.8501 (m-30) REVERT: K 110 CYS cc_start: 0.9259 (t) cc_final: 0.9044 (t) REVERT: K 115 LYS cc_start: 0.9798 (mmmt) cc_final: 0.9450 (mmmm) REVERT: K 123 ASP cc_start: 0.8662 (t70) cc_final: 0.7924 (t70) REVERT: K 125 GLN cc_start: 0.9624 (mt0) cc_final: 0.9414 (mm110) REVERT: M 64 GLU cc_start: 0.9366 (pp20) cc_final: 0.9152 (pp20) REVERT: M 92 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8810 (mt-10) REVERT: M 94 ASN cc_start: 0.9805 (t0) cc_final: 0.9415 (m-40) REVERT: M 112 GLN cc_start: 0.9506 (mm-40) cc_final: 0.9248 (mm110) REVERT: N 30 ARG cc_start: 0.8253 (mtt90) cc_final: 0.7789 (mtt-85) REVERT: N 59 MET cc_start: 0.9686 (mmt) cc_final: 0.9451 (tpp) REVERT: N 92 GLN cc_start: 0.9674 (tt0) cc_final: 0.9283 (pp30) REVERT: N 110 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8945 (mm-30) REVERT: L 43 VAL cc_start: 0.9243 (t) cc_final: 0.8954 (t) REVERT: L 49 LEU cc_start: 0.9581 (mm) cc_final: 0.8753 (tp) REVERT: L 84 MET cc_start: 0.9457 (mmm) cc_final: 0.9073 (mmp) REVERT: L 93 GLN cc_start: 0.9670 (tm-30) cc_final: 0.9375 (tm-30) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1237 time to fit residues: 51.9309 Evaluate side-chains 210 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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: 8.9990 chunk 105 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 162 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** 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** ** 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 = 0.3084 r_free = 0.3084 target = 0.040578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.027245 restraints weight = 169667.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028570 restraints weight = 81900.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.029465 restraints weight = 49056.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.029986 restraints weight = 33617.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030438 restraints weight = 25595.825| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 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 = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 19120 Z= 0.187 Angle : 0.724 11.778 27114 Z= 0.401 Chirality : 0.049 0.360 3080 Planarity : 0.004 0.047 2419 Dihedral : 29.998 172.650 4880 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -0.98 (0.21), residues: 1523 helix: 1.01 (0.21), residues: 585 sheet: -1.60 (0.28), residues: 303 loop : -1.73 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 76 TYR 0.018 0.002 TYR A 277 PHE 0.024 0.002 PHE H 61 TRP 0.018 0.002 TRP A 279 HIS 0.014 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 (19118) covalent geometry : angle 0.72419 / 0.40 (27114) hydrogen bonds : bond 0.07749 / 5.22 ( 982) hydrogen bonds : angle 4.67649 / 3.22 ( 2479) metal coordination : bond 0.00135 / 0.07 ( 1) Misc. bond : bond 0.00056 / 0.03 ( 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 279 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.576 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: A 26 MET cc_start: 0.8904 (mtm) cc_final: 0.8691 (mtm) REVERT: A 134 MET cc_start: 0.9281 (ttp) cc_final: 0.8881 (tmm) REVERT: A 242 MET cc_start: 0.9469 (ttm) cc_final: 0.9154 (ttp) REVERT: A 265 TYR cc_start: 0.9392 (m-80) cc_final: 0.9144 (m-80) REVERT: B 241 TRP cc_start: 0.8158 (m-10) cc_final: 0.7456 (m100) REVERT: C 3884 MET cc_start: 0.3052 (ppp) cc_final: 0.2130 (ttm) REVERT: G 54 TYR cc_start: 0.9275 (m-10) cc_final: 0.8936 (m-10) REVERT: G 61 LEU cc_start: 0.9588 (mm) cc_final: 0.8992 (mm) REVERT: G 67 PHE cc_start: 0.9695 (t80) cc_final: 0.9390 (t80) REVERT: G 70 LEU cc_start: 0.9684 (tp) cc_final: 0.9437 (tp) REVERT: G 84 PHE cc_start: 0.9348 (m-10) cc_final: 0.8756 (m-80) REVERT: G 90 MET cc_start: 0.9631 (mmp) cc_final: 0.9261 (mmm) REVERT: G 93 GLN cc_start: 0.9553 (tm-30) cc_final: 0.8084 (tm-30) REVERT: G 97 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8478 (mt-10) REVERT: G 99 TYR cc_start: 0.9648 (t80) cc_final: 0.9234 (t80) REVERT: G 103 LEU cc_start: 0.9782 (tt) cc_final: 0.9501 (mm) REVERT: G 106 ASP cc_start: 0.9597 (p0) cc_final: 0.9345 (p0) REVERT: H 49 LEU cc_start: 0.9508 (mt) cc_final: 0.9205 (mt) REVERT: H 52 GLU cc_start: 0.9033 (pm20) cc_final: 0.8416 (pm20) REVERT: H 53 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9133 (mm-30) REVERT: H 72 TYR cc_start: 0.9399 (m-80) cc_final: 0.9067 (m-80) REVERT: H 85 ASP cc_start: 0.9083 (m-30) cc_final: 0.8832 (m-30) REVERT: H 93 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8760 (tm-30) REVERT: I 41 GLU cc_start: 0.9385 (tt0) cc_final: 0.8746 (tm-30) REVERT: I 56 GLU cc_start: 0.9440 (tt0) cc_final: 0.8778 (mt-10) REVERT: I 64 GLU cc_start: 0.9556 (tt0) cc_final: 0.9272 (pt0) REVERT: I 83 LEU cc_start: 0.9654 (mp) cc_final: 0.9413 (mt) REVERT: I 95 LYS cc_start: 0.9606 (tptt) cc_final: 0.9342 (tppt) REVERT: J 65 ASP cc_start: 0.9321 (t70) cc_final: 0.9096 (t0) REVERT: J 76 ARG cc_start: 0.9569 (ttm110) cc_final: 0.9212 (ttm110) REVERT: J 92 GLN cc_start: 0.9685 (pt0) cc_final: 0.9320 (pp30) REVERT: J 102 GLU cc_start: 0.9165 (tp30) cc_final: 0.8884 (tm-30) REVERT: J 103 LEU cc_start: 0.9602 (mt) cc_final: 0.9308 (mt) REVERT: K 41 TYR cc_start: 0.9277 (m-80) cc_final: 0.8499 (m-80) REVERT: K 50 GLU cc_start: 0.9141 (tp30) cc_final: 0.8244 (tp30) REVERT: K 54 TYR cc_start: 0.9143 (m-10) cc_final: 0.7911 (m-10) REVERT: K 59 GLU cc_start: 0.9332 (pm20) cc_final: 0.9110 (pm20) REVERT: K 80 THR cc_start: 0.9564 (p) cc_final: 0.9005 (t) REVERT: K 81 ASP cc_start: 0.8697 (m-30) cc_final: 0.8404 (m-30) REVERT: K 110 CYS cc_start: 0.9289 (t) cc_final: 0.9037 (t) REVERT: K 115 LYS cc_start: 0.9811 (mmmt) cc_final: 0.9455 (mmmm) REVERT: K 123 ASP cc_start: 0.8506 (t70) cc_final: 0.7784 (t70) REVERT: K 124 ILE cc_start: 0.9802 (tp) cc_final: 0.9400 (tp) REVERT: K 125 GLN cc_start: 0.9617 (mt0) cc_final: 0.9396 (mm110) REVERT: M 38 ASN cc_start: 0.9483 (m110) cc_final: 0.9143 (p0) REVERT: M 64 GLU cc_start: 0.9327 (pp20) cc_final: 0.9078 (pp20) REVERT: M 94 ASN cc_start: 0.9794 (t0) cc_final: 0.9375 (m-40) REVERT: N 30 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7776 (mtt-85) REVERT: N 92 GLN cc_start: 0.9636 (tt0) cc_final: 0.9288 (pp30) REVERT: N 110 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8901 (mm-30) REVERT: L 43 VAL cc_start: 0.9222 (t) cc_final: 0.8915 (t) REVERT: L 45 ARG cc_start: 0.9288 (ttt-90) cc_final: 0.8948 (mmm-85) REVERT: L 49 LEU cc_start: 0.9542 (mm) cc_final: 0.8837 (tp) REVERT: L 74 GLU cc_start: 0.9361 (tm-30) cc_final: 0.9083 (tm-30) REVERT: L 93 GLN cc_start: 0.9670 (tm-30) cc_final: 0.9362 (tm-30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1252 time to fit residues: 53.7464 Evaluate side-chains 228 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 0.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027655 restraints weight = 168613.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.028995 restraints weight = 80983.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.029892 restraints weight = 48259.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030442 restraints weight = 32968.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.030848 restraints weight = 25038.089| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 19120 Z= 0.166 Angle : 0.713 11.823 27114 Z= 0.394 Chirality : 0.049 0.357 3080 Planarity : 0.004 0.043 2419 Dihedral : 29.898 173.614 4880 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1523 helix: 1.13 (0.21), residues: 581 sheet: -1.44 (0.28), residues: 300 loop : -1.68 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 76 TYR 0.015 0.002 TYR G 99 PHE 0.023 0.002 PHE H 61 TRP 0.020 0.002 TRP A 279 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (19118) covalent geometry : angle 0.71265 / 0.39 (27114) hydrogen bonds : bond 0.07138 / 4.79 ( 982) hydrogen bonds : angle 4.56640 / 3.14 ( 2479) metal coordination : bond 0.00113 / 0.06 ( 1) Misc. bond : bond 0.00038 / 0.02 ( 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 286 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.410 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: A 26 MET cc_start: 0.8906 (mtm) cc_final: 0.8693 (mtm) REVERT: A 134 MET cc_start: 0.9265 (ttp) cc_final: 0.8877 (tmm) REVERT: A 242 MET cc_start: 0.9465 (ttm) cc_final: 0.9141 (ttp) REVERT: A 265 TYR cc_start: 0.9369 (m-80) cc_final: 0.9138 (m-80) REVERT: A 273 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 277 TYR cc_start: 0.8903 (m-10) cc_final: 0.8644 (m-80) REVERT: B 241 TRP cc_start: 0.8209 (m-10) cc_final: 0.7492 (m100) REVERT: C 3884 MET cc_start: 0.2759 (ppp) cc_final: 0.1913 (ttm) REVERT: G 54 TYR cc_start: 0.9251 (m-10) cc_final: 0.8879 (m-10) REVERT: G 61 LEU cc_start: 0.9534 (mm) cc_final: 0.9037 (mm) REVERT: G 70 LEU cc_start: 0.9676 (tp) cc_final: 0.9471 (tp) REVERT: G 84 PHE cc_start: 0.9241 (m-10) cc_final: 0.8609 (m-80) REVERT: G 90 MET cc_start: 0.9640 (mmp) cc_final: 0.9272 (mmm) REVERT: G 103 LEU cc_start: 0.9774 (tt) cc_final: 0.9533 (mm) REVERT: H 49 LEU cc_start: 0.9485 (mt) cc_final: 0.9231 (mt) REVERT: H 52 GLU cc_start: 0.8983 (pm20) cc_final: 0.8393 (pm20) REVERT: H 53 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9194 (mm-30) REVERT: H 64 ASN cc_start: 0.9439 (m-40) cc_final: 0.9232 (m110) REVERT: H 72 TYR cc_start: 0.9417 (m-80) cc_final: 0.9053 (m-80) REVERT: H 84 MET cc_start: 0.9111 (mmm) cc_final: 0.8641 (mmm) REVERT: H 85 ASP cc_start: 0.9080 (m-30) cc_final: 0.8848 (m-30) REVERT: H 93 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8738 (tm-30) REVERT: I 41 GLU cc_start: 0.9384 (tt0) cc_final: 0.8739 (tm-30) REVERT: I 56 GLU cc_start: 0.9441 (tt0) cc_final: 0.8795 (mt-10) REVERT: I 64 GLU cc_start: 0.9549 (tt0) cc_final: 0.9311 (pt0) REVERT: I 95 LYS cc_start: 0.9595 (tptt) cc_final: 0.9320 (tppt) REVERT: J 65 ASP cc_start: 0.9266 (t70) cc_final: 0.9048 (t0) REVERT: J 76 ARG cc_start: 0.9613 (ttm110) cc_final: 0.9121 (ttm110) REVERT: J 92 GLN cc_start: 0.9661 (pt0) cc_final: 0.9306 (pp30) REVERT: J 97 LEU cc_start: 0.9581 (mm) cc_final: 0.9327 (mm) REVERT: J 102 GLU cc_start: 0.9154 (tp30) cc_final: 0.8898 (tm-30) REVERT: J 103 LEU cc_start: 0.9595 (mt) cc_final: 0.9317 (mt) REVERT: K 41 TYR cc_start: 0.9268 (m-80) cc_final: 0.8485 (m-80) REVERT: K 50 GLU cc_start: 0.9164 (tp30) cc_final: 0.8417 (tp30) REVERT: K 54 TYR cc_start: 0.9144 (m-10) cc_final: 0.8011 (m-10) REVERT: K 59 GLU cc_start: 0.9392 (pm20) cc_final: 0.9184 (pm20) REVERT: K 62 ILE cc_start: 0.9539 (mm) cc_final: 0.9279 (mm) REVERT: K 73 GLU cc_start: 0.8747 (tt0) cc_final: 0.8526 (pt0) REVERT: K 80 THR cc_start: 0.9565 (p) cc_final: 0.9085 (t) REVERT: K 81 ASP cc_start: 0.8714 (m-30) cc_final: 0.8425 (m-30) REVERT: K 110 CYS cc_start: 0.9338 (t) cc_final: 0.9077 (t) REVERT: K 115 LYS cc_start: 0.9812 (mmmt) cc_final: 0.9482 (mmmm) REVERT: K 123 ASP cc_start: 0.8517 (t70) cc_final: 0.7701 (t70) REVERT: M 38 ASN cc_start: 0.9421 (m110) cc_final: 0.9121 (p0) REVERT: M 64 GLU cc_start: 0.9280 (pp20) cc_final: 0.9001 (pp20) REVERT: M 90 ASP cc_start: 0.9567 (t70) cc_final: 0.9357 (t70) REVERT: M 94 ASN cc_start: 0.9784 (t0) cc_final: 0.9374 (m-40) REVERT: M 112 GLN cc_start: 0.9379 (mm-40) cc_final: 0.9176 (mm110) REVERT: N 30 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7750 (mtt-85) REVERT: N 92 GLN cc_start: 0.9634 (tt0) cc_final: 0.9264 (pp30) REVERT: N 110 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8931 (mm-30) REVERT: L 43 VAL cc_start: 0.9174 (t) cc_final: 0.8712 (t) REVERT: L 45 ARG cc_start: 0.9296 (ttt-90) cc_final: 0.8966 (ttp80) REVERT: L 74 GLU cc_start: 0.9383 (tm-30) cc_final: 0.9105 (tm-30) REVERT: L 93 GLN cc_start: 0.9675 (tm-30) cc_final: 0.9460 (tm-30) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1342 time to fit residues: 58.4928 Evaluate side-chains 232 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 6.9990 chunk 133 optimal weight: 0.0770 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.027050 restraints weight = 173768.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.028354 restraints weight = 84013.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029235 restraints weight = 50433.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029745 restraints weight = 34625.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030188 restraints weight = 26436.151| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 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 = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 19120 Z= 0.229 Angle : 0.737 12.440 27114 Z= 0.408 Chirality : 0.048 0.339 3080 Planarity : 0.004 0.044 2419 Dihedral : 29.890 172.922 4880 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.08 % Allowed : 0.46 % 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: -0.88 (0.21), residues: 1523 helix: 1.05 (0.21), residues: 583 sheet: -1.47 (0.28), residues: 307 loop : -1.66 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 92 TYR 0.025 0.002 TYR G 99 PHE 0.041 0.002 PHE K 67 TRP 0.014 0.002 TRP A 279 HIS 0.012 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.23 (19118) covalent geometry : angle 0.73661 / 0.41 (27114) hydrogen bonds : bond 0.08349 / 5.62 ( 982) hydrogen bonds : angle 4.71352 / 3.24 ( 2479) metal coordination : bond 0.00148 / 0.08 ( 1) Misc. bond : bond 0.00065 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3472.69 seconds wall clock time: 60 minutes 47.67 seconds (3647.67 seconds total)