Starting phenix.real_space_refine on Thu Jul 2 17:07:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2026/7f04_31396.map" } resolution = 2.86 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= 0.002 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 7 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5832 2.51 5 N 1519 2.21 5 O 1527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8934 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.78, per 1000 atoms: 0.20 Number of scatterers: 8934 At special positions: 0 Unit cell: (98.176, 96.512, 118.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 46 16.00 P 7 15.00 Mg 2 11.99 O 1527 8.00 N 1519 7.00 C 5832 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: 0.64 Conformation dependent library (CDL) restraints added in 293.0 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 68.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.567A pdb=" N GLN A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.871A pdb=" N TYR A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.900A pdb=" N ALA A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 158 through 176 removed outlier: 3.660A pdb=" N GLY A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.563A pdb=" N ILE B 6 " --> pdb=" O MET B 2 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 22 through 35 removed outlier: 3.980A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 42 through 76 Proline residue: B 51 - end of helix removed outlier: 3.617A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 111 removed outlier: 4.140A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.968A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 143 Proline residue: B 138 - end of helix removed outlier: 3.790A pdb=" N GLY B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 158 through 165 removed outlier: 3.529A pdb=" N LEU B 161 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 165 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.629A pdb=" N THR B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.502A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 40 removed outlier: 4.119A pdb=" N GLN C 16 " --> pdb=" O PRO C 12 " (cutoff:3.500A) Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 56 through 84 Proline residue: C 62 - end of helix removed outlier: 3.696A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 120 removed outlier: 3.559A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 148 Processing helix chain 'C' and resid 156 through 185 Proline residue: C 171 - end of helix removed outlier: 3.570A pdb=" N HIS C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 229 removed outlier: 3.780A pdb=" N LEU C 202 " --> pdb=" O MET C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.495A pdb=" N GLU C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 53 Proline residue: D 31 - end of helix Processing helix chain 'E' and resid 39 through 48 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 105 through 115 removed outlier: 3.882A pdb=" N GLU E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 128 through 138 removed outlier: 4.077A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 158 through 176 removed outlier: 3.540A pdb=" N GLN E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY E 176 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 21 through 39 removed outlier: 4.114A pdb=" N LEU F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 42 through 66 Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 67 through 69 No H-bonds generated for 'chain 'F' and resid 67 through 69' Processing helix chain 'F' and resid 70 through 75 removed outlier: 3.753A pdb=" N LEU F 74 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 70 through 75' Processing helix chain 'F' and resid 88 through 111 removed outlier: 3.612A pdb=" N VAL F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 122 through 152 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 160 through 165 removed outlier: 3.532A pdb=" N LEU F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 165' Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 185 removed outlier: 3.613A pdb=" N MET F 185 " --> pdb=" O ASP F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 220 removed outlier: 3.564A pdb=" N LEU F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Proline residue: F 208 - end of helix removed outlier: 3.767A pdb=" N GLN F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.135A pdb=" N LEU A 16 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ARG A 11 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A 18 " --> pdb=" O CYS A 9 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N CYS A 9 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 2 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.135A pdb=" N LEU A 16 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ARG A 11 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A 18 " --> pdb=" O CYS A 9 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N CYS A 9 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 7 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 55 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.383A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP A 151 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP A 29 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 197 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN A 31 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.178A pdb=" N LEU E 16 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ARG E 11 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.178A pdb=" N LEU E 16 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ARG E 11 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU E 7 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA E 55 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.051A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP E 151 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE E 79 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP E 148 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR E 182 " --> pdb=" O TRP E 148 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU E 150 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP E 29 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE E 197 " --> pdb=" O TRP E 29 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN E 31 " --> pdb=" O ILE E 197 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2856 1.36 - 1.53: 5918 1.53 - 1.71: 287 1.71 - 1.88: 87 1.88 - 2.06: 4 Bond restraints: 9152 Sorted by residual: bond pdb=" C4 ATP A 301 " pdb=" C5 ATP A 301 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 ATP A 301 " pdb=" C6 ATP A 301 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.19e+01 bond pdb=" C8 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.16e+01 ... (remaining 9147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 12408 3.88 - 7.76: 85 7.76 - 11.64: 9 11.64 - 15.53: 2 15.53 - 19.41: 2 Bond angle restraints: 12506 Sorted by residual: angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 121.32 18.55 1.00e+00 1.00e+00 3.44e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 123.70 13.13 1.00e+00 1.00e+00 1.72e+02 angle pdb=" PA ATP A 301 " pdb=" O3A ATP A 301 " pdb=" PB ATP A 301 " ideal model delta sigma weight residual 136.83 124.75 12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" C5 ATP A 301 " pdb=" C4 ATP A 301 " pdb=" N3 ATP A 301 " ideal model delta sigma weight residual 126.80 118.24 8.56 1.00e+00 1.00e+00 7.32e+01 ... (remaining 12501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 4727 15.97 - 31.94: 469 31.94 - 47.91: 96 47.91 - 63.87: 15 63.87 - 79.84: 6 Dihedral angle restraints: 5313 sinusoidal: 2089 harmonic: 3224 Sorted by residual: dihedral pdb=" CA LEU A 127 " pdb=" C LEU A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual 180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ILE C 10 " pdb=" C ILE C 10 " pdb=" N PRO C 11 " pdb=" CA PRO C 11 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LEU C 154 " pdb=" C LEU C 154 " pdb=" N ALA C 155 " pdb=" CA ALA C 155 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 902 0.032 - 0.064: 372 0.064 - 0.096: 122 0.096 - 0.128: 57 0.128 - 0.160: 10 Chirality restraints: 1463 Sorted by residual: chirality pdb=" CB ILE C 10 " pdb=" CA ILE C 10 " pdb=" CG1 ILE C 10 " pdb=" CG2 ILE C 10 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CB THR E 15 " pdb=" CA THR E 15 " pdb=" OG1 THR E 15 " pdb=" CG2 THR E 15 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE A 149 " pdb=" N ILE A 149 " pdb=" C ILE A 149 " pdb=" CB ILE A 149 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1460 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " -0.075 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO B 113 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 82 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO E 83 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 11 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 12 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 12 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 12 " 0.023 5.00e-02 4.00e+02 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 25 2.34 - 2.98: 4291 2.98 - 3.62: 13729 3.62 - 4.26: 21285 4.26 - 4.90: 36191 Nonbonded interactions: 75521 Sorted by model distance: nonbonded pdb="MG MG A 300 " pdb=" O3G ATP A 301 " model vdw 1.706 2.170 nonbonded pdb="MG MG A 300 " pdb=" O2B ATP A 301 " model vdw 1.780 2.170 nonbonded pdb="MG MG E 300 " pdb=" O2B ATP E 301 " model vdw 1.795 2.170 nonbonded pdb=" OG1 THR A 41 " pdb="MG MG A 300 " model vdw 1.985 2.170 nonbonded pdb=" OG1 THR E 41 " pdb="MG MG E 300 " model vdw 2.014 2.170 ... (remaining 75516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.420 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.008 0.598 9153 Z= 0.295 Angle : 0.801 19.408 12506 Z= 0.492 Chirality : 0.043 0.160 1463 Planarity : 0.006 0.109 1529 Dihedral : 13.218 79.843 3229 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.04 (0.26), residues: 1118 helix: 0.64 (0.20), residues: 693 sheet: -1.34 (0.69), residues: 54 loop : -0.97 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 71 TYR 0.016 0.001 TYR C 15 PHE 0.022 0.001 PHE B 3 TRP 0.026 0.002 TRP E 78 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.29 ( 9152) covalent geometry : angle 0.80077 / 0.49 (12506) hydrogen bonds : bond 0.19346 / 12.91 ( 513) hydrogen bonds : angle 6.83319 / 4.74 ( 1482) Misc. bond : bond 0.59751 / 31.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.317 Fit side-chains REVERT: B 2 MET cc_start: 0.5527 (mtm) cc_final: 0.5307 (tpt) REVERT: E 28 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7507 (mm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.4853 time to fit residues: 73.8799 Evaluate side-chains 121 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 17 HIS C 185 GLN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143621 restraints weight = 9695.040| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.30 r_work: 0.3556 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.290 9153 Z= 0.142 Angle : 0.657 8.637 12506 Z= 0.323 Chirality : 0.042 0.181 1463 Planarity : 0.005 0.057 1529 Dihedral : 6.762 81.995 1249 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 2.07 % Allowed : 9.71 % Favored : 88.22 % 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: 0.57 (0.26), residues: 1118 helix: 1.25 (0.20), residues: 701 sheet: -1.39 (0.69), residues: 54 loop : -0.99 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 71 TYR 0.010 0.001 TYR C 15 PHE 0.022 0.001 PHE B 3 TRP 0.017 0.001 TRP B 55 HIS 0.004 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9152) covalent geometry : angle 0.65675 / 0.32 (12506) hydrogen bonds : bond 0.04206 / 2.85 ( 513) hydrogen bonds : angle 4.75006 / 3.33 ( 1482) Misc. bond : bond 0.28991 / 15.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.306 Fit side-chains REVERT: B 2 MET cc_start: 0.6381 (mtm) cc_final: 0.5338 (tpt) REVERT: B 71 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7602 (ttm-80) REVERT: C 8 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.5233 (mp) REVERT: C 86 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7055 (mtt) REVERT: C 190 MET cc_start: 0.2328 (pmt) cc_final: 0.1103 (ptp) REVERT: E 1 MET cc_start: 0.8167 (mmt) cc_final: 0.7773 (mmm) REVERT: E 28 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7661 (mm-30) REVERT: E 57 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7171 (pt0) REVERT: F 1 MET cc_start: 0.6871 (ttp) cc_final: 0.6607 (tmm) outliers start: 19 outliers final: 8 residues processed: 133 average time/residue: 0.5050 time to fit residues: 71.6632 Evaluate side-chains 133 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 108 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** 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 = 0.3787 r_free = 0.3787 target = 0.154304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139574 restraints weight = 9680.123| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.35 r_work: 0.3503 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 9153 Z= 0.125 Angle : 0.617 8.845 12506 Z= 0.300 Chirality : 0.041 0.197 1463 Planarity : 0.005 0.044 1529 Dihedral : 6.461 83.811 1249 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.40 % Allowed : 12.00 % Favored : 85.61 % 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: 0.96 (0.26), residues: 1118 helix: 1.68 (0.20), residues: 694 sheet: -1.21 (0.70), residues: 54 loop : -1.08 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 71 TYR 0.008 0.001 TYR C 71 PHE 0.019 0.001 PHE B 3 TRP 0.017 0.001 TRP B 55 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9152) covalent geometry : angle 0.61675 / 0.30 (12506) hydrogen bonds : bond 0.03611 / 2.45 ( 513) hydrogen bonds : angle 4.40392 / 3.11 ( 1482) Misc. bond : bond 0.22340 / 11.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.227 Fit side-chains REVERT: B 2 MET cc_start: 0.6523 (mtm) cc_final: 0.5384 (tpt) REVERT: B 71 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7600 (ttm-80) REVERT: C 8 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5379 (mp) REVERT: C 86 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6981 (mtt) REVERT: C 190 MET cc_start: 0.2222 (pmt) cc_final: 0.1110 (ptp) REVERT: E -1 MET cc_start: 0.5221 (OUTLIER) cc_final: 0.4659 (mpp) REVERT: E 1 MET cc_start: 0.8230 (mmt) cc_final: 0.7778 (mmm) REVERT: E 5 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6501 (mtt180) REVERT: E 28 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7595 (mm-30) REVERT: E 57 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: F 1 MET cc_start: 0.6942 (ttp) cc_final: 0.6557 (tmm) REVERT: F 10 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7478 (mm-30) outliers start: 22 outliers final: 5 residues processed: 129 average time/residue: 0.4340 time to fit residues: 60.0217 Evaluate side-chains 130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 167 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 ASN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136715 restraints weight = 9710.834| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.36 r_work: 0.3444 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 9153 Z= 0.150 Angle : 0.640 10.184 12506 Z= 0.310 Chirality : 0.043 0.223 1463 Planarity : 0.005 0.045 1529 Dihedral : 6.397 83.637 1249 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 2.84 % Allowed : 13.63 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1118 helix: 1.64 (0.20), residues: 706 sheet: -0.84 (0.73), residues: 50 loop : -1.00 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.009 0.001 TYR C 71 PHE 0.016 0.001 PHE B 3 TRP 0.017 0.001 TRP B 55 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9152) covalent geometry : angle 0.63955 / 0.31 (12506) hydrogen bonds : bond 0.03696 / 2.50 ( 513) hydrogen bonds : angle 4.28253 / 3.03 ( 1482) Misc. bond : bond 0.20700 / 10.89 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.269 Fit side-chains REVERT: B 2 MET cc_start: 0.6681 (mtm) cc_final: 0.5516 (tpt) REVERT: B 71 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7742 (ttm-80) REVERT: C 8 LEU cc_start: 0.5732 (OUTLIER) cc_final: 0.5489 (mp) REVERT: C 86 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7060 (mtt) REVERT: C 190 MET cc_start: 0.2380 (pmt) cc_final: 0.1302 (ptp) REVERT: E -1 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.4954 (mpp) REVERT: E 1 MET cc_start: 0.8251 (mmt) cc_final: 0.7603 (mmm) REVERT: E 28 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7633 (mm-30) REVERT: E 57 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: F 1 MET cc_start: 0.6962 (ttp) cc_final: 0.6615 (tmm) REVERT: F 10 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7567 (mm-30) REVERT: F 117 MET cc_start: 0.7594 (mtp) cc_final: 0.7184 (tpp) outliers start: 26 outliers final: 9 residues processed: 140 average time/residue: 0.4162 time to fit residues: 62.4937 Evaluate side-chains 137 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139910 restraints weight = 9714.732| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.33 r_work: 0.3514 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 9153 Z= 0.141 Angle : 0.631 8.912 12506 Z= 0.306 Chirality : 0.042 0.217 1463 Planarity : 0.005 0.046 1529 Dihedral : 6.369 84.960 1249 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 3.49 % Allowed : 14.07 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.26), residues: 1118 helix: 1.75 (0.20), residues: 704 sheet: -0.77 (0.74), residues: 50 loop : -1.04 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.008 0.001 TYR C 71 PHE 0.016 0.001 PHE B 3 TRP 0.018 0.001 TRP B 55 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9152) covalent geometry : angle 0.63114 / 0.31 (12506) hydrogen bonds : bond 0.03465 / 2.35 ( 513) hydrogen bonds : angle 4.22578 / 3.00 ( 1482) Misc. bond : bond 0.19238 / 10.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.211 Fit side-chains REVERT: B 2 MET cc_start: 0.6493 (mtm) cc_final: 0.5302 (tpt) REVERT: B 71 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7692 (ttm-80) REVERT: C 8 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5568 (mp) REVERT: C 86 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6837 (mtt) REVERT: C 190 MET cc_start: 0.2401 (pmt) cc_final: 0.1473 (ptp) REVERT: E -1 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.4891 (mpp) REVERT: E 1 MET cc_start: 0.8183 (mmt) cc_final: 0.7503 (mmm) REVERT: E 3 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: E 28 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7577 (mm-30) REVERT: E 57 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: E 175 GLN cc_start: 0.7112 (pt0) cc_final: 0.6601 (mp10) REVERT: F 1 MET cc_start: 0.6957 (ttp) cc_final: 0.6543 (tmm) REVERT: F 10 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7527 (mm-30) REVERT: F 117 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7143 (tpp) outliers start: 32 outliers final: 11 residues processed: 143 average time/residue: 0.3859 time to fit residues: 59.4174 Evaluate side-chains 141 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136073 restraints weight = 9694.895| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.33 r_work: 0.3462 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 9153 Z= 0.205 Angle : 0.690 10.248 12506 Z= 0.335 Chirality : 0.044 0.223 1463 Planarity : 0.005 0.052 1529 Dihedral : 6.583 85.102 1249 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 3.93 % Allowed : 15.16 % Favored : 80.92 % 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: 0.88 (0.26), residues: 1118 helix: 1.55 (0.20), residues: 711 sheet: -0.80 (0.75), residues: 50 loop : -1.16 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 16 TYR 0.011 0.001 TYR F 192 PHE 0.015 0.002 PHE B 3 TRP 0.018 0.002 TRP F 55 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 ( 9152) covalent geometry : angle 0.69024 / 0.34 (12506) hydrogen bonds : bond 0.03988 / 2.69 ( 513) hydrogen bonds : angle 4.30363 / 3.05 ( 1482) Misc. bond : bond 0.21372 / 11.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.340 Fit side-chains REVERT: B 2 MET cc_start: 0.6621 (mtm) cc_final: 0.5431 (tpt) REVERT: C 86 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6982 (mtt) REVERT: E -1 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.4947 (mpp) REVERT: E 28 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7804 (mm-30) REVERT: E 175 GLN cc_start: 0.7122 (pt0) cc_final: 0.6609 (mp10) REVERT: F 1 MET cc_start: 0.7011 (ttp) cc_final: 0.6563 (tmm) REVERT: F 10 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7599 (mm-30) REVERT: F 117 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7219 (tpp) outliers start: 36 outliers final: 13 residues processed: 142 average time/residue: 0.4529 time to fit residues: 68.8180 Evaluate side-chains 139 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.0370 chunk 91 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142017 restraints weight = 9738.081| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.33 r_work: 0.3540 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.176 9153 Z= 0.114 Angle : 0.616 10.400 12506 Z= 0.298 Chirality : 0.041 0.251 1463 Planarity : 0.005 0.056 1529 Dihedral : 6.342 88.699 1249 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 1.96 % Allowed : 17.67 % Favored : 80.37 % 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: 1.21 (0.26), residues: 1118 helix: 1.86 (0.20), residues: 707 sheet: -0.69 (0.75), residues: 50 loop : -1.13 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 196 TYR 0.007 0.001 TYR C 15 PHE 0.016 0.001 PHE B 3 TRP 0.020 0.001 TRP B 55 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9152) covalent geometry : angle 0.61614 / 0.30 (12506) hydrogen bonds : bond 0.03101 / 2.10 ( 513) hydrogen bonds : angle 4.12814 / 2.94 ( 1482) Misc. bond : bond 0.17645 / 9.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.184 Fit side-chains REVERT: B 2 MET cc_start: 0.6417 (mtm) cc_final: 0.5265 (tpt) REVERT: C 86 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6826 (mtt) REVERT: E -1 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4879 (mpp) REVERT: E 1 MET cc_start: 0.8139 (mmt) cc_final: 0.7493 (mmm) REVERT: E 28 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7604 (mm-30) REVERT: E 57 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: E 175 GLN cc_start: 0.7037 (pt0) cc_final: 0.6517 (mp10) REVERT: F 1 MET cc_start: 0.6971 (ttp) cc_final: 0.6542 (tmm) REVERT: F 10 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7529 (mm-30) REVERT: F 117 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7242 (tpp) outliers start: 18 outliers final: 9 residues processed: 134 average time/residue: 0.4266 time to fit residues: 61.2421 Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139582 restraints weight = 9620.574| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.32 r_work: 0.3517 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 9153 Z= 0.152 Angle : 0.656 12.137 12506 Z= 0.315 Chirality : 0.043 0.241 1463 Planarity : 0.005 0.058 1529 Dihedral : 6.374 88.145 1249 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 2.40 % Allowed : 17.88 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1118 helix: 1.85 (0.20), residues: 704 sheet: -0.71 (0.75), residues: 50 loop : -1.12 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 196 TYR 0.010 0.001 TYR F 192 PHE 0.012 0.001 PHE B 3 TRP 0.018 0.001 TRP C 84 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9152) covalent geometry : angle 0.65627 / 0.32 (12506) hydrogen bonds : bond 0.03490 / 2.36 ( 513) hydrogen bonds : angle 4.15118 / 2.94 ( 1482) Misc. bond : bond 0.19690 / 10.36 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.310 Fit side-chains REVERT: B 2 MET cc_start: 0.6305 (mtm) cc_final: 0.5191 (tpt) REVERT: C 86 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6822 (mtt) REVERT: E -1 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.4950 (mpp) REVERT: E 28 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7600 (mm-30) REVERT: E 57 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: E 175 GLN cc_start: 0.7067 (pt0) cc_final: 0.6557 (mp10) REVERT: F 1 MET cc_start: 0.6983 (ttp) cc_final: 0.6549 (tmm) REVERT: F 10 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7514 (mm-30) REVERT: F 16 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.6552 (mtm180) REVERT: F 117 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7189 (tpp) outliers start: 22 outliers final: 11 residues processed: 130 average time/residue: 0.4747 time to fit residues: 65.8514 Evaluate side-chains 136 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS D 38 HIS F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138469 restraints weight = 9681.789| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.33 r_work: 0.3487 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 9153 Z= 0.163 Angle : 0.671 12.893 12506 Z= 0.323 Chirality : 0.043 0.246 1463 Planarity : 0.005 0.062 1529 Dihedral : 6.457 88.439 1249 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.99 % Favored : 93.83 % Rotamer: Outliers : 2.07 % Allowed : 18.32 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1118 helix: 1.76 (0.20), residues: 707 sheet: -0.73 (0.75), residues: 50 loop : -1.16 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 196 TYR 0.015 0.001 TYR F 192 PHE 0.013 0.001 PHE B 3 TRP 0.018 0.001 TRP B 55 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 9152) covalent geometry : angle 0.67074 / 0.32 (12506) hydrogen bonds : bond 0.03634 / 2.46 ( 513) hydrogen bonds : angle 4.19214 / 2.97 ( 1482) Misc. bond : bond 0.20480 / 10.78 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.209 Fit side-chains REVERT: B 2 MET cc_start: 0.6198 (mtm) cc_final: 0.5171 (tpt) REVERT: B 87 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7520 (pt) REVERT: C 86 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6837 (mtt) REVERT: E -1 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4987 (mpp) REVERT: E 28 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7639 (mm-30) REVERT: E 57 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7009 (pm20) REVERT: E 175 GLN cc_start: 0.7055 (pt0) cc_final: 0.6555 (mp10) REVERT: F 1 MET cc_start: 0.6986 (ttp) cc_final: 0.6549 (tmm) REVERT: F 10 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7558 (mm-30) REVERT: F 117 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7197 (tpp) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.4371 time to fit residues: 62.5274 Evaluate side-chains 137 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139557 restraints weight = 9619.279| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.32 r_work: 0.3500 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 9153 Z= 0.146 Angle : 0.663 11.630 12506 Z= 0.318 Chirality : 0.042 0.245 1463 Planarity : 0.005 0.061 1529 Dihedral : 6.432 89.979 1249 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 2.18 % Allowed : 18.21 % Favored : 79.61 % 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: 1.14 (0.26), residues: 1118 helix: 1.80 (0.20), residues: 707 sheet: -0.78 (0.76), residues: 50 loop : -1.14 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 196 TYR 0.014 0.001 TYR F 192 PHE 0.015 0.001 PHE B 3 TRP 0.018 0.001 TRP B 55 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9152) covalent geometry : angle 0.66343 / 0.32 (12506) hydrogen bonds : bond 0.03486 / 2.36 ( 513) hydrogen bonds : angle 4.16272 / 2.95 ( 1482) Misc. bond : bond 0.19717 / 10.38 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.256 Fit side-chains REVERT: A 104 THR cc_start: 0.7431 (m) cc_final: 0.7129 (t) REVERT: B 2 MET cc_start: 0.6126 (mtm) cc_final: 0.5072 (tpt) REVERT: B 87 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7448 (pt) REVERT: B 124 TYR cc_start: 0.8055 (t80) cc_final: 0.7761 (t80) REVERT: B 185 MET cc_start: 0.7530 (tmm) cc_final: 0.7188 (tmt) REVERT: C 86 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6818 (mtt) REVERT: E -1 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.4979 (mpp) REVERT: E 28 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7624 (mm-30) REVERT: E 57 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: E 175 GLN cc_start: 0.7043 (pt0) cc_final: 0.6528 (mp10) REVERT: F 1 MET cc_start: 0.6956 (ttp) cc_final: 0.6526 (tmm) REVERT: F 10 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7557 (mm-30) REVERT: F 117 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7217 (tpp) outliers start: 20 outliers final: 10 residues processed: 135 average time/residue: 0.4331 time to fit residues: 62.5401 Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136849 restraints weight = 9525.973| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.31 r_work: 0.3471 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 9153 Z= 0.189 Angle : 0.704 12.397 12506 Z= 0.338 Chirality : 0.044 0.245 1463 Planarity : 0.005 0.059 1529 Dihedral : 6.581 89.755 1249 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.53 % Favored : 93.29 % Rotamer: Outliers : 1.96 % Allowed : 18.54 % Favored : 79.50 % 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: 0.95 (0.26), residues: 1118 helix: 1.63 (0.20), residues: 708 sheet: -0.79 (0.77), residues: 50 loop : -1.18 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 196 TYR 0.017 0.001 TYR F 192 PHE 0.021 0.001 PHE B 3 TRP 0.018 0.002 TRP F 55 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 9152) covalent geometry : angle 0.70400 / 0.34 (12506) hydrogen bonds : bond 0.03871 / 2.62 ( 513) hydrogen bonds : angle 4.24863 / 3.01 ( 1482) Misc. bond : bond 0.21305 / 11.21 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2383.29 seconds wall clock time: 41 minutes 19.26 seconds (2479.26 seconds total)