Starting phenix.real_space_refine on Wed Sep 17 15:27:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f04_31396/09_2025/7f04_31396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f04_31396/09_2025/7f04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f04_31396/09_2025/7f04_31396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f04_31396/09_2025/7f04_31396.map" model { file = "/net/cci-nas-00/data/ceres_data/7f04_31396/09_2025/7f04_31396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f04_31396/09_2025/7f04_31396.cif" } 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-2.0-5805/lib/python3.9/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: 2.42, per 1000 atoms: 0.27 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: 1.07 Conformation dependent library (CDL) restraints added in 339.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.25 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: 1.43 Time building geometry restraints manager: 1.22 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: 4754 15.97 - 31.94: 490 31.94 - 47.91: 112 47.91 - 63.87: 23 63.87 - 79.84: 8 Dihedral angle restraints: 5387 sinusoidal: 2163 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 5384 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: 2.520 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.080 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 13.871 79.843 3303 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 aren 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 covalent geometry : bond 0.00508 ( 9152) covalent geometry : angle 0.80077 (12506) hydrogen bonds : bond 0.19346 ( 513) hydrogen bonds : angle 6.83319 ( 1482) Misc. bond : bond 0.59751 ( 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 : 0.391 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: 0.6490 time to fit residues: 98.5738 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 : 0.342 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS A 185 GLN B 17 HIS C 185 GLN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143855 restraints weight = 9702.536| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.30 r_work: 0.3563 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.283 9153 Z= 0.142 Angle : 0.655 8.301 12506 Z= 0.322 Chirality : 0.042 0.178 1463 Planarity : 0.005 0.055 1529 Dihedral : 9.310 82.236 1323 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.36 % Rotamer: Outliers : 1.96 % Allowed : 10.03 % Favored : 88.00 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1118 helix: 1.24 (0.20), residues: 701 sheet: -1.41 (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 0.011 0.001 TYR C 15 PHE 0.021 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 covalent geometry : bond 0.00320 ( 9152) covalent geometry : angle 0.65501 (12506) hydrogen bonds : bond 0.04057 ( 513) hydrogen bonds : angle 4.70739 ( 1482) Misc. bond : bond 0.28258 ( 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 146 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.310 Fit side-chains REVERT: B 2 MET cc_start: 0.6380 (mtm) cc_final: 0.5345 (tpt) REVERT: B 71 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7585 (ttm-80) REVERT: C 8 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.5237 (mp) REVERT: C 86 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7045 (mtt) REVERT: C 190 MET cc_start: 0.2221 (pmt) cc_final: 0.1066 (ptp) REVERT: E 1 MET cc_start: 0.8198 (mmt) cc_final: 0.7798 (mmm) REVERT: E 28 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7662 (mm-30) REVERT: E 57 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: F 1 MET cc_start: 0.6871 (ttp) cc_final: 0.6612 (tmm) REVERT: F 10 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7510 (mm-30) outliers start: 18 outliers final: 7 residues processed: 133 average time/residue: 0.6500 time to fit residues: 91.8647 Evaluate side-chains 132 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137866 restraints weight = 9680.694| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.35 r_work: 0.3485 rms_B_bonded: 1.95 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: 0.8209 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.224 9153 Z= 0.139 Angle : 0.629 8.694 12506 Z= 0.307 Chirality : 0.042 0.228 1463 Planarity : 0.005 0.044 1529 Dihedral : 9.049 83.322 1323 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.73 % Allowed : 12.00 % Favored : 85.28 % 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 aren not related in a simple way. whole: 0.90 (0.26), residues: 1118 helix: 1.55 (0.20), residues: 705 sheet: -0.98 (0.72), residues: 50 loop : -1.05 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 71 TYR 0.008 0.001 TYR C 71 PHE 0.018 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 covalent geometry : bond 0.00321 ( 9152) covalent geometry : angle 0.62947 (12506) hydrogen bonds : bond 0.03760 ( 513) hydrogen bonds : angle 4.39666 ( 1482) Misc. bond : bond 0.22432 ( 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 150 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.354 Fit side-chains REVERT: B 2 MET cc_start: 0.6571 (mtm) cc_final: 0.5405 (tpt) REVERT: B 71 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7654 (ttm-80) REVERT: C 8 LEU cc_start: 0.5632 (OUTLIER) cc_final: 0.5411 (mp) REVERT: C 86 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7031 (mtt) REVERT: C 190 MET cc_start: 0.2381 (pmt) cc_final: 0.1217 (ptp) REVERT: E -1 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4690 (mpp) REVERT: E 5 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6547 (mtt180) REVERT: E 28 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7619 (mm-30) REVERT: E 57 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: F 1 MET cc_start: 0.6964 (ttp) cc_final: 0.6572 (tmm) REVERT: F 10 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7536 (mm-30) REVERT: F 117 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7199 (tpp) outliers start: 25 outliers final: 8 residues processed: 130 average time/residue: 0.5918 time to fit residues: 82.3064 Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 192 SER Chi-restraints excluded: chain A residue 197 ILE 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 Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL 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: 0.9990 chunk 3 optimal weight: 0.0670 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136656 restraints weight = 9740.165| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.36 r_work: 0.3446 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 9153 Z= 0.151 Angle : 0.641 10.075 12506 Z= 0.310 Chirality : 0.042 0.215 1463 Planarity : 0.005 0.042 1529 Dihedral : 9.055 84.037 1323 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 3.05 % Allowed : 13.85 % Favored : 83.10 % 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 aren not related in a simple way. whole: 0.99 (0.26), residues: 1118 helix: 1.62 (0.20), residues: 706 sheet: -0.94 (0.72), residues: 50 loop : -1.02 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 E 73 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9152) covalent geometry : angle 0.64149 (12506) hydrogen bonds : bond 0.03620 ( 513) hydrogen bonds : angle 4.28469 ( 1482) Misc. bond : bond 0.20264 ( 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 157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.362 Fit side-chains REVERT: B 1 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4839 (mtt) REVERT: B 2 MET cc_start: 0.6702 (mtm) cc_final: 0.5510 (tpt) REVERT: C 8 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5355 (mp) REVERT: C 86 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7080 (mtt) REVERT: C 190 MET cc_start: 0.2280 (pmt) cc_final: 0.1290 (ptp) REVERT: E -1 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.4961 (mpp) REVERT: E 1 MET cc_start: 0.8279 (mmt) cc_final: 0.7633 (mmm) REVERT: E 28 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7650 (mm-30) REVERT: E 57 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: F 1 MET cc_start: 0.7008 (ttp) cc_final: 0.6627 (tmm) REVERT: F 10 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7625 (mm-30) REVERT: F 117 MET cc_start: 0.7720 (mtp) cc_final: 0.7251 (tpp) outliers start: 28 outliers final: 8 residues processed: 138 average time/residue: 0.6287 time to fit residues: 92.2645 Evaluate side-chains 138 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 1 MET 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 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: 2.9990 chunk 108 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 93 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138236 restraints weight = 9735.960| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.32 r_work: 0.3499 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 9153 Z= 0.162 Angle : 0.651 8.826 12506 Z= 0.316 Chirality : 0.043 0.221 1463 Planarity : 0.005 0.046 1529 Dihedral : 9.087 84.755 1323 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.99 % Favored : 93.83 % Rotamer: Outliers : 3.93 % Allowed : 14.07 % Favored : 82.01 % 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 aren not related in a simple way. whole: 1.01 (0.26), residues: 1118 helix: 1.65 (0.20), residues: 706 sheet: -0.89 (0.73), residues: 50 loop : -1.04 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 71 TYR 0.009 0.001 TYR F 192 PHE 0.016 0.001 PHE B 3 TRP 0.019 0.001 TRP B 55 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9152) covalent geometry : angle 0.65109 (12506) hydrogen bonds : bond 0.03653 ( 513) hydrogen bonds : angle 4.26959 ( 1482) Misc. bond : bond 0.20354 ( 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 164 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.364 Fit side-chains REVERT: B 1 MET cc_start: 0.5260 (OUTLIER) cc_final: 0.5043 (mtt) REVERT: B 2 MET cc_start: 0.6519 (mtm) cc_final: 0.5350 (tpt) REVERT: C 8 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5544 (mp) REVERT: C 86 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6855 (mtt) REVERT: C 190 MET cc_start: 0.2434 (pmt) cc_final: 0.1440 (ptp) REVERT: E -1 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.4898 (mpp) REVERT: E 3 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: E 28 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7625 (mm-30) REVERT: E 57 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7016 (pm20) REVERT: E 175 GLN cc_start: 0.7084 (pt0) cc_final: 0.6544 (mp10) REVERT: F 1 MET cc_start: 0.6978 (ttp) cc_final: 0.6542 (tmm) REVERT: F 10 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7570 (mm-30) REVERT: F 117 MET cc_start: 0.7697 (mtp) cc_final: 0.7185 (tpp) outliers start: 36 outliers final: 11 residues processed: 145 average time/residue: 0.5612 time to fit residues: 86.8956 Evaluate side-chains 142 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 1 MET 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 104 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 79 LEU 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: 4.9990 chunk 99 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135752 restraints weight = 9678.408| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.32 r_work: 0.3459 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 9153 Z= 0.208 Angle : 0.694 11.143 12506 Z= 0.337 Chirality : 0.045 0.227 1463 Planarity : 0.005 0.051 1529 Dihedral : 9.213 85.632 1323 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.26 % Favored : 93.56 % Rotamer: Outliers : 3.38 % Allowed : 15.49 % Favored : 81.13 % 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 aren not related in a simple way. whole: 0.82 (0.26), residues: 1118 helix: 1.52 (0.20), residues: 708 sheet: -0.90 (0.73), residues: 50 loop : -1.21 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 71 TYR 0.012 0.001 TYR F 192 PHE 0.014 0.002 PHE B 3 TRP 0.019 0.002 TRP F 55 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9152) covalent geometry : angle 0.69396 (12506) hydrogen bonds : bond 0.04015 ( 513) hydrogen bonds : angle 4.33061 ( 1482) Misc. bond : bond 0.21516 ( 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 153 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.335 Fit side-chains REVERT: B 2 MET cc_start: 0.6650 (mtm) cc_final: 0.5491 (tpt) REVERT: B 87 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7653 (pt) REVERT: C 86 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6995 (mtt) REVERT: C 152 ARG cc_start: 0.7277 (mmt180) cc_final: 0.7013 (mmt180) REVERT: E -1 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5014 (mpp) REVERT: E 28 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7682 (mm-30) REVERT: F 117 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7202 (tpp) outliers start: 31 outliers final: 12 residues processed: 137 average time/residue: 0.6297 time to fit residues: 91.7149 Evaluate side-chains 140 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 87 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 104 THR 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: 5.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139633 restraints weight = 9761.812| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.33 r_work: 0.3506 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1799 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= 0.127 Angle : 0.622 8.588 12506 Z= 0.302 Chirality : 0.041 0.244 1463 Planarity : 0.005 0.058 1529 Dihedral : 9.064 88.023 1323 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.84 % Allowed : 16.90 % Favored : 80.26 % 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 aren not related in a simple way. whole: 1.11 (0.26), residues: 1118 helix: 1.79 (0.20), residues: 704 sheet: -0.79 (0.75), residues: 50 loop : -1.15 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 196 TYR 0.008 0.001 TYR F 192 PHE 0.015 0.001 PHE B 3 TRP 0.020 0.001 TRP B 55 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9152) covalent geometry : angle 0.62201 (12506) hydrogen bonds : bond 0.03297 ( 513) hydrogen bonds : angle 4.18520 ( 1482) Misc. bond : bond 0.19224 ( 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 152 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.330 Fit side-chains REVERT: B 2 MET cc_start: 0.6465 (mtm) cc_final: 0.5322 (tpt) REVERT: C 86 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6789 (mtt) REVERT: E -1 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.4876 (mpp) REVERT: E 28 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7665 (mm-30) REVERT: E 57 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: E 175 GLN cc_start: 0.7058 (pt0) cc_final: 0.6563 (mp10) REVERT: F 1 MET cc_start: 0.6981 (ttp) cc_final: 0.6547 (tmm) REVERT: F 10 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7558 (mm-30) REVERT: F 117 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7199 (tpp) outliers start: 26 outliers final: 9 residues processed: 136 average time/residue: 0.5950 time to fit residues: 86.2789 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 : 0.314 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 82 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138909 restraints weight = 9673.121| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.33 r_work: 0.3493 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 9153 Z= 0.142 Angle : 0.646 12.100 12506 Z= 0.311 Chirality : 0.042 0.241 1463 Planarity : 0.005 0.062 1529 Dihedral : 8.878 88.478 1323 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 2.40 % Allowed : 17.67 % Favored : 79.93 % 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 aren not related in a simple way. whole: 1.14 (0.26), residues: 1118 helix: 1.78 (0.20), residues: 709 sheet: -0.82 (0.75), residues: 50 loop : -1.10 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 196 TYR 0.011 0.001 TYR F 192 PHE 0.015 0.001 PHE B 3 TRP 0.018 0.001 TRP B 101 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9152) covalent geometry : angle 0.64629 (12506) hydrogen bonds : bond 0.03431 ( 513) hydrogen bonds : angle 4.18090 ( 1482) Misc. bond : bond 0.19945 ( 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 145 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.266 Fit side-chains REVERT: B 2 MET cc_start: 0.6488 (mtm) cc_final: 0.5405 (tpt) REVERT: B 87 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7548 (pt) REVERT: C 86 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6844 (mtt) REVERT: E -1 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.4847 (mpp) REVERT: E 28 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7649 (mm-30) REVERT: E 57 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: E 175 GLN cc_start: 0.7062 (pt0) cc_final: 0.6557 (mp10) REVERT: F 1 MET cc_start: 0.6998 (ttp) cc_final: 0.6571 (tmm) REVERT: F 10 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7541 (mm-30) REVERT: F 117 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7194 (tpp) outliers start: 22 outliers final: 12 residues processed: 132 average time/residue: 0.6046 time to fit residues: 85.0112 Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 C residue 182 THR 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 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=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: 2.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137956 restraints weight = 9714.052| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.33 r_work: 0.3483 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 9153 Z= 0.159 Angle : 0.655 11.487 12506 Z= 0.317 Chirality : 0.043 0.240 1463 Planarity : 0.005 0.063 1529 Dihedral : 8.876 88.988 1323 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.17 % Favored : 93.65 % Rotamer: Outliers : 2.29 % Allowed : 18.10 % 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 aren not related in a simple way. whole: 1.08 (0.26), residues: 1118 helix: 1.74 (0.20), residues: 708 sheet: -0.85 (0.75), residues: 50 loop : -1.13 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 196 TYR 0.015 0.001 TYR F 192 PHE 0.014 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 covalent geometry : bond 0.00380 ( 9152) covalent geometry : angle 0.65547 (12506) hydrogen bonds : bond 0.03568 ( 513) hydrogen bonds : angle 4.21074 ( 1482) Misc. bond : bond 0.20367 ( 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: 21 poor density : 123 time to evaluate : 0.360 Fit side-chains REVERT: B 2 MET cc_start: 0.6498 (mtm) cc_final: 0.5402 (tpt) REVERT: B 87 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7578 (pt) REVERT: B 124 TYR cc_start: 0.8087 (t80) cc_final: 0.7793 (t80) REVERT: C 86 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6904 (mtt) REVERT: E -1 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.4950 (mpp) REVERT: E 28 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7673 (mm-30) REVERT: E 57 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: E 175 GLN cc_start: 0.7082 (pt0) cc_final: 0.6578 (mp10) REVERT: F 1 MET cc_start: 0.6988 (ttp) cc_final: 0.6559 (tmm) REVERT: F 10 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7566 (mm-30) REVERT: F 117 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7200 (tpp) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 0.6357 time to fit residues: 89.0350 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 : 0.329 ------------------------------------------------------------------------------- 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 87 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 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 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 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: 0.8980 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137959 restraints weight = 9622.160| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.31 r_work: 0.3497 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 9153 Z= 0.158 Angle : 0.656 11.622 12506 Z= 0.317 Chirality : 0.043 0.245 1463 Planarity : 0.005 0.062 1529 Dihedral : 8.876 89.984 1323 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.17 % Favored : 93.65 % Rotamer: Outliers : 2.29 % Allowed : 18.10 % 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 aren not related in a simple way. whole: 1.08 (0.26), residues: 1118 helix: 1.74 (0.20), residues: 707 sheet: -0.99 (0.75), residues: 50 loop : -1.11 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 196 TYR 0.013 0.001 TYR F 192 PHE 0.014 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 covalent geometry : bond 0.00378 ( 9152) covalent geometry : angle 0.65599 (12506) hydrogen bonds : bond 0.03547 ( 513) hydrogen bonds : angle 4.20009 ( 1482) Misc. bond : bond 0.20344 ( 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 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.397 Fit side-chains REVERT: B 2 MET cc_start: 0.6447 (mtm) cc_final: 0.5343 (tpt) REVERT: B 87 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7569 (pt) REVERT: B 124 TYR cc_start: 0.8078 (t80) cc_final: 0.7780 (t80) REVERT: C 86 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6903 (mtt) REVERT: E -1 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.4967 (mpp) REVERT: E 28 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7677 (mm-30) REVERT: E 57 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: E 175 GLN cc_start: 0.7079 (pt0) cc_final: 0.6573 (mp10) REVERT: F 1 MET cc_start: 0.7010 (ttp) cc_final: 0.6583 (tmm) REVERT: F 10 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7554 (mm-30) REVERT: F 117 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7218 (tpp) outliers start: 21 outliers final: 11 residues processed: 133 average time/residue: 0.5928 time to fit residues: 84.0607 Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 C residue 182 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 105 optimal weight: 0.0030 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139794 restraints weight = 9512.018| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.30 r_work: 0.3519 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 9153 Z= 0.134 Angle : 0.636 9.699 12506 Z= 0.307 Chirality : 0.042 0.243 1463 Planarity : 0.005 0.058 1529 Dihedral : 8.809 87.884 1323 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % 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 aren not related in a simple way. whole: 1.15 (0.26), residues: 1118 helix: 1.85 (0.20), residues: 701 sheet: -1.02 (0.76), residues: 50 loop : -1.14 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 196 TYR 0.013 0.001 TYR F 192 PHE 0.014 0.001 PHE B 3 TRP 0.019 0.001 TRP B 55 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9152) covalent geometry : angle 0.63632 (12506) hydrogen bonds : bond 0.03320 ( 513) hydrogen bonds : angle 4.15367 ( 1482) Misc. bond : bond 0.19258 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2962.93 seconds wall clock time: 51 minutes 15.15 seconds (3075.15 seconds total)