Starting phenix.real_space_refine on Sun Jul 27 13:44:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f04_31396/07_2025/7f04_31396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f04_31396/07_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_31396/07_2025/7f04_31396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2025/7f04_31396.map" model { file = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2025/7f04_31396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f04_31396/07_2025/7f04_31396.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.63, per 1000 atoms: 0.74 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.89 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: 2.62 Time building geometry restraints manager: 2.78 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: 1.910 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.180 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.002 TRP E 78 HIS 0.005 0.001 HIS A 73 PHE 0.022 0.001 PHE B 3 TYR 0.016 0.001 TYR C 15 ARG 0.009 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.19346 ( 513) hydrogen bonds : angle 6.83319 ( 1482) covalent geometry : bond 0.00508 ( 9152) covalent geometry : angle 0.80077 (12506) 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 : 0.931 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: 1.3102 time to fit residues: 199.5400 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 : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.155112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141010 restraints weight = 9591.912| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.28 r_work: 0.3527 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.281 9153 Z= 0.184 Angle : 0.690 9.456 12506 Z= 0.340 Chirality : 0.044 0.180 1463 Planarity : 0.006 0.055 1529 Dihedral : 9.385 81.452 1323 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.81 % Favored : 94.01 % Rotamer: Outliers : 2.29 % Allowed : 9.38 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1118 helix: 1.13 (0.20), residues: 701 sheet: -1.11 (0.73), residues: 50 loop : -1.04 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 55 HIS 0.006 0.001 HIS E 96 PHE 0.020 0.001 PHE B 142 TYR 0.011 0.001 TYR C 15 ARG 0.007 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 513) hydrogen bonds : angle 4.81999 ( 1482) covalent geometry : bond 0.00434 ( 9152) covalent geometry : angle 0.69010 (12506) Misc. bond : bond 0.28075 ( 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 150 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.928 Fit side-chains REVERT: B 2 MET cc_start: 0.6387 (mtm) cc_final: 0.5375 (tpt) REVERT: C 8 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.5142 (mp) REVERT: C 86 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7076 (mtt) REVERT: E -1 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.4688 (mpp) REVERT: E 1 MET cc_start: 0.8208 (mmt) cc_final: 0.7824 (mmm) REVERT: E 28 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7733 (mm-30) REVERT: E 57 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7197 (pt0) REVERT: F 1 MET cc_start: 0.7012 (ttp) cc_final: 0.6642 (tmm) outliers start: 21 outliers final: 7 residues processed: 133 average time/residue: 1.2889 time to fit residues: 182.7704 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 : 0.983 ------------------------------------------------------------------------------- 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 102 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 E residue -1 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.152534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137864 restraints weight = 9676.610| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.35 r_work: 0.3456 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 9153 Z= 0.136 Angle : 0.635 9.207 12506 Z= 0.309 Chirality : 0.042 0.201 1463 Planarity : 0.005 0.043 1529 Dihedral : 9.140 83.263 1323 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.62 % Allowed : 12.21 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1118 helix: 1.44 (0.20), residues: 708 sheet: -1.05 (0.73), residues: 50 loop : -1.05 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 55 HIS 0.004 0.001 HIS B 100 PHE 0.019 0.001 PHE B 3 TYR 0.008 0.001 TYR C 71 ARG 0.006 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 513) hydrogen bonds : angle 4.46428 ( 1482) covalent geometry : bond 0.00315 ( 9152) covalent geometry : angle 0.63468 (12506) Misc. bond : bond 0.22195 ( 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 149 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.970 Fit side-chains REVERT: A 82 GLN cc_start: 0.7970 (mm110) cc_final: 0.7690 (mm110) REVERT: B 2 MET cc_start: 0.6597 (mtm) cc_final: 0.5474 (tpt) REVERT: C 8 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.5232 (mp) REVERT: C 86 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7086 (mtt) REVERT: C 190 MET cc_start: 0.2278 (pmt) cc_final: 0.1095 (ptp) REVERT: E -1 MET cc_start: 0.5279 (OUTLIER) cc_final: 0.4688 (mpp) REVERT: E 28 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 57 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: F 1 MET cc_start: 0.6950 (ttp) cc_final: 0.6540 (tmm) REVERT: F 10 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7582 (mm-30) outliers start: 24 outliers final: 9 residues processed: 130 average time/residue: 1.1330 time to fit residues: 158.0052 Evaluate side-chains 136 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 -1 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 167 GLN 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 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132249 restraints weight = 9674.099| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.39 r_work: 0.3417 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.223 9153 Z= 0.225 Angle : 0.708 10.031 12506 Z= 0.346 Chirality : 0.045 0.220 1463 Planarity : 0.006 0.048 1529 Dihedral : 9.364 83.139 1323 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.53 % Favored : 93.29 % Rotamer: Outliers : 3.82 % Allowed : 12.87 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1118 helix: 1.24 (0.20), residues: 711 sheet: -0.90 (0.67), residues: 62 loop : -1.18 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.015 0.002 PHE B 3 TYR 0.014 0.002 TYR F 192 ARG 0.006 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 513) hydrogen bonds : angle 4.45284 ( 1482) covalent geometry : bond 0.00543 ( 9152) covalent geometry : angle 0.70762 (12506) Misc. bond : bond 0.22296 ( 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 162 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.916 Fit side-chains REVERT: A 82 GLN cc_start: 0.7911 (mm110) cc_final: 0.7590 (mm110) REVERT: B 2 MET cc_start: 0.6767 (mtm) cc_final: 0.5467 (tpt) REVERT: C 8 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5484 (mp) REVERT: C 86 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7044 (mtt) REVERT: E -1 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.4975 (mpp) REVERT: E 28 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7717 (mm-30) REVERT: F 76 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.6276 (p0) REVERT: F 117 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7126 (tpp) outliers start: 35 outliers final: 11 residues processed: 141 average time/residue: 1.2217 time to fit residues: 183.9823 Evaluate side-chains 144 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 44 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 2 MET Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 117 MET 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 91 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.152288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137786 restraints weight = 9588.618| |-----------------------------------------------------------------------------| r_work (start): 0.3602 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: 3.35 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1644 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= 0.146 Angle : 0.644 8.451 12506 Z= 0.314 Chirality : 0.042 0.219 1463 Planarity : 0.005 0.045 1529 Dihedral : 9.252 85.296 1323 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 3.49 % Allowed : 15.27 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1118 helix: 1.55 (0.20), residues: 704 sheet: -1.07 (0.73), residues: 50 loop : -1.19 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 55 HIS 0.003 0.001 HIS A 73 PHE 0.015 0.001 PHE B 3 TYR 0.008 0.001 TYR C 71 ARG 0.008 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 513) hydrogen bonds : angle 4.30478 ( 1482) covalent geometry : bond 0.00343 ( 9152) covalent geometry : angle 0.64370 (12506) Misc. bond : bond 0.20342 ( 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 : 1.107 Fit side-chains REVERT: A 82 GLN cc_start: 0.7990 (mm110) cc_final: 0.7676 (mm110) REVERT: B 2 MET cc_start: 0.6510 (mtm) cc_final: 0.5392 (tpt) REVERT: B 87 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7599 (pt) REVERT: B 206 LEU cc_start: 0.8277 (mp) cc_final: 0.8044 (mm) REVERT: C 8 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5428 (mp) REVERT: C 86 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6870 (mtt) REVERT: E -1 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.4863 (mpp) REVERT: E 1 MET cc_start: 0.8171 (mmt) cc_final: 0.7510 (mmm) REVERT: E 28 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7698 (mm-30) REVERT: E 57 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: F 1 MET cc_start: 0.6975 (ttp) cc_final: 0.6524 (tmm) REVERT: F 10 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7611 (mm-30) REVERT: F 117 MET cc_start: 0.7594 (mtp) cc_final: 0.7142 (tpp) outliers start: 32 outliers final: 8 residues processed: 140 average time/residue: 1.1819 time to fit residues: 177.4090 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 : 0.974 ------------------------------------------------------------------------------- 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 8 LEU 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 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 84 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.148642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134153 restraints weight = 9636.633| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.31 r_work: 0.3441 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.224 9153 Z= 0.236 Angle : 0.707 9.748 12506 Z= 0.346 Chirality : 0.045 0.217 1463 Planarity : 0.006 0.051 1529 Dihedral : 9.377 85.211 1323 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.71 % Favored : 93.11 % Rotamer: Outliers : 4.47 % Allowed : 14.72 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1118 helix: 1.40 (0.20), residues: 702 sheet: -1.03 (0.73), residues: 50 loop : -1.25 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.014 0.002 PHE B 3 TYR 0.013 0.002 TYR F 192 ARG 0.008 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 513) hydrogen bonds : angle 4.39424 ( 1482) covalent geometry : bond 0.00570 ( 9152) covalent geometry : angle 0.70661 (12506) Misc. bond : bond 0.22425 ( 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 164 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.964 Fit side-chains REVERT: B 1 MET cc_start: 0.5086 (OUTLIER) cc_final: 0.4084 (mmm) REVERT: B 2 MET cc_start: 0.6714 (mtm) cc_final: 0.5511 (tpt) REVERT: B 87 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7658 (pt) REVERT: B 185 MET cc_start: 0.7219 (mpp) cc_final: 0.6983 (tmm) REVERT: C 8 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5534 (mp) REVERT: C 86 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7019 (mtt) REVERT: C 152 ARG cc_start: 0.7413 (mmt180) cc_final: 0.7114 (mmt180) REVERT: E -1 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.5203 (mpp) REVERT: E 28 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7728 (mm-30) REVERT: F 71 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6994 (ttm-80) REVERT: F 117 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7224 (tpp) outliers start: 41 outliers final: 15 residues processed: 141 average time/residue: 1.3006 time to fit residues: 195.1949 Evaluate side-chains 143 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 1 MET 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 8 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 44 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 2 MET Chi-restraints excluded: chain F residue 71 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.151937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137518 restraints weight = 9702.933| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.31 r_work: 0.3493 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1795 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= 0.148 Angle : 0.647 8.561 12506 Z= 0.315 Chirality : 0.042 0.239 1463 Planarity : 0.005 0.056 1529 Dihedral : 9.274 87.184 1323 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.08 % Favored : 93.74 % Rotamer: Outliers : 3.38 % Allowed : 16.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1118 helix: 1.61 (0.20), residues: 702 sheet: -1.08 (0.74), residues: 50 loop : -1.21 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 55 HIS 0.003 0.001 HIS A 73 PHE 0.014 0.001 PHE B 3 TYR 0.010 0.001 TYR F 192 ARG 0.005 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 513) hydrogen bonds : angle 4.27027 ( 1482) covalent geometry : bond 0.00351 ( 9152) covalent geometry : angle 0.64676 (12506) Misc. bond : bond 0.20443 ( 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 157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.019 Fit side-chains REVERT: A 82 GLN cc_start: 0.8214 (mm110) cc_final: 0.7870 (mm-40) REVERT: B 1 MET cc_start: 0.5257 (OUTLIER) cc_final: 0.4152 (mmm) REVERT: B 2 MET cc_start: 0.6548 (mtm) cc_final: 0.5403 (tpt) REVERT: B 87 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7599 (pt) REVERT: C 86 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6986 (mtt) REVERT: E -1 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.5011 (mpp) REVERT: E 28 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7711 (mm-30) REVERT: E 57 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: E 175 GLN cc_start: 0.7114 (pt0) cc_final: 0.6631 (mp10) REVERT: F 117 MET cc_start: 0.7645 (mtp) cc_final: 0.7231 (tpp) outliers start: 31 outliers final: 16 residues processed: 140 average time/residue: 1.3264 time to fit residues: 198.4218 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 : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 189 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 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 228 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 44 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 2 MET 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 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.153670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139190 restraints weight = 9807.656| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.33 r_work: 0.3510 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1892 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= 0.129 Angle : 0.624 8.683 12506 Z= 0.303 Chirality : 0.042 0.251 1463 Planarity : 0.005 0.061 1529 Dihedral : 9.179 88.941 1323 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 2.73 % Allowed : 17.88 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1118 helix: 1.77 (0.20), residues: 703 sheet: -1.08 (0.75), residues: 50 loop : -1.18 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 55 HIS 0.004 0.001 HIS A 73 PHE 0.016 0.001 PHE B 3 TYR 0.009 0.001 TYR F 192 ARG 0.008 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 513) hydrogen bonds : angle 4.16179 ( 1482) covalent geometry : bond 0.00300 ( 9152) covalent geometry : angle 0.62445 (12506) Misc. bond : bond 0.19685 ( 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 149 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.003 Fit side-chains REVERT: A 82 GLN cc_start: 0.8155 (mm110) cc_final: 0.7809 (mm-40) REVERT: B 2 MET cc_start: 0.6439 (mtm) cc_final: 0.5337 (tpt) REVERT: B 87 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7553 (pt) REVERT: C 86 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6836 (mtt) REVERT: E -1 MET cc_start: 0.5483 (OUTLIER) cc_final: 0.4873 (mpp) REVERT: E 28 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7660 (mm-30) REVERT: E 57 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: E 175 GLN cc_start: 0.7069 (pt0) cc_final: 0.6582 (mp10) REVERT: F 1 MET cc_start: 0.6983 (ttp) cc_final: 0.6566 (tmm) REVERT: F 117 MET cc_start: 0.7639 (mtp) cc_final: 0.7231 (tpp) outliers start: 25 outliers final: 13 residues processed: 135 average time/residue: 1.3332 time to fit residues: 191.5712 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 : 0.987 ------------------------------------------------------------------------------- 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 E residue -1 MET Chi-restraints excluded: chain E residue 44 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 84 LEU 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 107 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.151040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136490 restraints weight = 9731.610| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.32 r_work: 0.3470 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1874 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= 0.179 Angle : 0.674 12.013 12506 Z= 0.326 Chirality : 0.044 0.243 1463 Planarity : 0.005 0.064 1529 Dihedral : 9.276 88.205 1323 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.26 % Favored : 93.56 % Rotamer: Outliers : 2.94 % Allowed : 17.88 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1118 helix: 1.64 (0.20), residues: 705 sheet: -1.06 (0.75), residues: 50 loop : -1.24 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 55 HIS 0.004 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.012 0.001 TYR F 192 ARG 0.007 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 513) hydrogen bonds : angle 4.24745 ( 1482) covalent geometry : bond 0.00430 ( 9152) covalent geometry : angle 0.67357 (12506) Misc. bond : bond 0.21341 ( 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 148 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.165 Fit side-chains REVERT: A 82 GLN cc_start: 0.8169 (mm110) cc_final: 0.7816 (mm-40) REVERT: B 1 MET cc_start: 0.5091 (OUTLIER) cc_final: 0.4724 (mtt) REVERT: B 2 MET cc_start: 0.6503 (mtm) cc_final: 0.5428 (tpt) REVERT: B 87 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7671 (pt) REVERT: B 185 MET cc_start: 0.7502 (tmm) cc_final: 0.7190 (tmt) REVERT: C 86 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: E -1 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5072 (mpp) REVERT: E 28 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7682 (mm-30) REVERT: E 57 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: E 175 GLN cc_start: 0.7085 (pt0) cc_final: 0.6604 (mp10) REVERT: F 71 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7045 (ttm-80) REVERT: F 117 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7241 (tpp) outliers start: 27 outliers final: 12 residues processed: 133 average time/residue: 1.4681 time to fit residues: 208.6370 Evaluate side-chains 139 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 1 MET 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 44 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 71 ARG 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 29 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.150714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135648 restraints weight = 9701.694| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.42 r_work: 0.3444 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 9153 Z= 0.118 Angle : 0.628 11.621 12506 Z= 0.303 Chirality : 0.041 0.250 1463 Planarity : 0.005 0.063 1529 Dihedral : 9.046 88.462 1323 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 2.51 % Allowed : 18.54 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1118 helix: 1.82 (0.20), residues: 705 sheet: -1.07 (0.76), residues: 50 loop : -1.21 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 55 HIS 0.004 0.001 HIS A 73 PHE 0.016 0.001 PHE B 3 TYR 0.010 0.001 TYR F 192 ARG 0.007 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 513) hydrogen bonds : angle 4.13263 ( 1482) covalent geometry : bond 0.00267 ( 9152) covalent geometry : angle 0.62816 (12506) Misc. bond : bond 0.18578 ( 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 147 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.893 Fit side-chains REVERT: A 82 GLN cc_start: 0.8113 (mm110) cc_final: 0.7762 (mm-40) REVERT: B 1 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.4871 (mtp) REVERT: B 2 MET cc_start: 0.6330 (mtm) cc_final: 0.5182 (tpt) REVERT: B 87 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7488 (pt) REVERT: B 124 TYR cc_start: 0.8053 (t80) cc_final: 0.7764 (t80) REVERT: C 86 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6792 (mtt) REVERT: D 11 PHE cc_start: 0.6308 (m-80) cc_final: 0.5930 (m-80) REVERT: E -1 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.4808 (mpp) REVERT: E 1 MET cc_start: 0.8137 (mmt) cc_final: 0.7415 (mmm) REVERT: E 28 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7580 (mm-30) REVERT: E 57 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: E 175 GLN cc_start: 0.7040 (pt0) cc_final: 0.6491 (mp10) REVERT: F 1 MET cc_start: 0.6927 (ttp) cc_final: 0.6460 (tmm) REVERT: F 71 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7224 (ttm-80) REVERT: F 117 MET cc_start: 0.7598 (mtp) cc_final: 0.7172 (tpp) outliers start: 23 outliers final: 11 residues processed: 135 average time/residue: 1.4058 time to fit residues: 202.4919 Evaluate side-chains 139 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 87 LEU 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 F residue 71 ARG 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 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138683 restraints weight = 9672.469| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.32 r_work: 0.3494 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 9153 Z= 0.146 Angle : 0.648 11.505 12506 Z= 0.313 Chirality : 0.043 0.250 1463 Planarity : 0.005 0.059 1529 Dihedral : 8.962 88.503 1323 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 2.07 % Allowed : 19.08 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1118 helix: 1.76 (0.20), residues: 707 sheet: -0.97 (0.77), residues: 50 loop : -1.18 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 179 HIS 0.004 0.001 HIS A 73 PHE 0.014 0.001 PHE B 3 TYR 0.012 0.001 TYR F 192 ARG 0.009 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 513) hydrogen bonds : angle 4.15316 ( 1482) covalent geometry : bond 0.00347 ( 9152) covalent geometry : angle 0.64828 (12506) Misc. bond : bond 0.19821 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6679.56 seconds wall clock time: 117 minutes 24.64 seconds (7044.64 seconds total)