Starting phenix.real_space_refine on Fri Mar 14 00:59:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f04_31396/03_2025/7f04_31396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f04_31396/03_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_31396/03_2025/7f04_31396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f04_31396/03_2025/7f04_31396.map" model { file = "/net/cci-nas-00/data/ceres_data/7f04_31396/03_2025/7f04_31396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f04_31396/03_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-5624/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: 5.87, per 1000 atoms: 0.66 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: 2.19 Conformation dependent library (CDL) restraints added in 926.6 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 68.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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: 2.54 Time building geometry restraints manager: 2.58 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: 1.880 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.170 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- 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 : 0.005 0.085 9152 Z= 0.334 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 *********************** 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 : 0.999 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: 1.2658 time to fit residues: 193.1820 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 : 0.962 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 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: 0.7756 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.157120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142978 restraints weight = 9576.990| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.29 r_work: 0.3553 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9152 Z= 0.229 Angle : 0.666 9.486 12506 Z= 0.327 Chirality : 0.043 0.177 1463 Planarity : 0.005 0.054 1529 Dihedral : 9.336 81.775 1323 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 2.18 % Allowed : 9.71 % Favored : 88.11 % 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: 0.53 (0.26), residues: 1118 helix: 1.21 (0.20), residues: 701 sheet: -1.39 (0.69), residues: 54 loop : -1.00 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.005 0.001 HIS E 96 PHE 0.021 0.001 PHE B 3 TYR 0.011 0.001 TYR C 15 ARG 0.008 0.000 ARG B 71 *********************** 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 149 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.966 Fit side-chains REVERT: B 2 MET cc_start: 0.6365 (mtm) cc_final: 0.5334 (tpt) REVERT: B 71 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7606 (ttm-80) REVERT: C 8 LEU cc_start: 0.5469 (OUTLIER) cc_final: 0.5195 (mp) REVERT: C 86 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7060 (mtt) REVERT: E -1 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4673 (mpp) REVERT: E 28 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7692 (mm-30) REVERT: E 57 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: F 1 MET cc_start: 0.6975 (ttp) cc_final: 0.6605 (tmm) outliers start: 20 outliers final: 8 residues processed: 133 average time/residue: 1.1960 time to fit residues: 169.7996 Evaluate side-chains 135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 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 64 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 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: 4.9990 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.151765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137021 restraints weight = 9658.311| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.35 r_work: 0.3447 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9152 Z= 0.234 Angle : 0.642 8.800 12506 Z= 0.313 Chirality : 0.042 0.198 1463 Planarity : 0.005 0.043 1529 Dihedral : 9.111 82.942 1323 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.26 % Favored : 93.56 % Rotamer: Outliers : 2.62 % Allowed : 11.67 % Favored : 85.71 % 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: 0.81 (0.26), residues: 1118 helix: 1.50 (0.20), residues: 704 sheet: -1.07 (0.73), residues: 50 loop : -1.10 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 55 HIS 0.004 0.001 HIS A 73 PHE 0.018 0.001 PHE B 3 TYR 0.008 0.001 TYR C 71 ARG 0.006 0.000 ARG B 71 *********************** 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 148 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.018 Fit side-chains REVERT: A 193 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8210 (mtpm) REVERT: B 2 MET cc_start: 0.6609 (mtm) cc_final: 0.5481 (tpt) REVERT: B 71 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7723 (ttm-80) REVERT: C 8 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.5283 (mp) REVERT: C 86 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7073 (mtt) REVERT: C 190 MET cc_start: 0.2409 (pmt) cc_final: 0.1150 (ptp) REVERT: E -1 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.4764 (mpp) REVERT: E 28 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7699 (mm-30) REVERT: E 57 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6919 (pm20) REVERT: F 1 MET cc_start: 0.6950 (ttp) cc_final: 0.6562 (tmm) REVERT: F 10 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7605 (mm-30) outliers start: 24 outliers final: 8 residues processed: 128 average time/residue: 1.2193 time to fit residues: 166.9688 Evaluate side-chains 133 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 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 E residue 167 GLN Chi-restraints excluded: chain F residue 2 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 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.152867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138121 restraints weight = 9625.817| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.35 r_work: 0.3462 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9152 Z= 0.204 Angle : 0.619 8.430 12506 Z= 0.300 Chirality : 0.042 0.223 1463 Planarity : 0.005 0.041 1529 Dihedral : 9.030 84.500 1323 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.94 % Allowed : 13.85 % Favored : 83.21 % 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: 1.04 (0.26), residues: 1118 helix: 1.69 (0.20), residues: 704 sheet: -1.01 (0.73), residues: 50 loop : -1.05 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.003 0.001 HIS E 73 PHE 0.016 0.001 PHE B 3 TYR 0.008 0.001 TYR C 71 ARG 0.003 0.000 ARG B 16 *********************** 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 152 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.008 Fit side-chains REVERT: B 2 MET cc_start: 0.6660 (mtm) cc_final: 0.5472 (tpt) REVERT: B 71 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7746 (ttm-80) REVERT: C 8 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5515 (mp) REVERT: C 86 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6973 (mtt) REVERT: C 190 MET cc_start: 0.2303 (pmt) cc_final: 0.1236 (ptp) REVERT: E -1 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.4915 (mpp) REVERT: E 1 MET cc_start: 0.8245 (mmt) cc_final: 0.7606 (mmm) REVERT: E 28 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7636 (mm-30) REVERT: E 57 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: F 1 MET cc_start: 0.6976 (ttp) cc_final: 0.6592 (tmm) REVERT: F 10 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7548 (mm-30) REVERT: F 76 ASP cc_start: 0.6132 (OUTLIER) cc_final: 0.5926 (p0) REVERT: F 117 MET cc_start: 0.7571 (mtp) cc_final: 0.7135 (tpp) outliers start: 27 outliers final: 8 residues processed: 134 average time/residue: 1.1063 time to fit residues: 159.3983 Evaluate side-chains 134 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 76 ASP 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: 3.9990 chunk 54 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.148577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133979 restraints weight = 9660.399| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.32 r_work: 0.3438 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9152 Z= 0.408 Angle : 0.736 11.114 12506 Z= 0.357 Chirality : 0.046 0.208 1463 Planarity : 0.006 0.048 1529 Dihedral : 9.338 83.946 1323 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.71 % Favored : 93.11 % Rotamer: Outliers : 4.14 % Allowed : 14.29 % Favored : 81.57 % 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: 0.61 (0.25), residues: 1118 helix: 1.30 (0.20), residues: 712 sheet: -0.82 (0.66), residues: 62 loop : -1.23 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 55 HIS 0.006 0.001 HIS A 73 PHE 0.014 0.002 PHE B 3 TYR 0.012 0.002 TYR F 192 ARG 0.004 0.001 ARG A 168 *********************** 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 165 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.260 Fit side-chains REVERT: A 109 GLU cc_start: 0.8373 (tp30) cc_final: 0.7896 (tp30) REVERT: A 193 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8190 (mtmt) REVERT: B 2 MET cc_start: 0.6800 (mtm) cc_final: 0.5556 (tpt) REVERT: C 8 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5545 (mp) REVERT: C 86 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7056 (mtt) REVERT: E -1 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.5003 (mpp) REVERT: E 28 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7837 (mm-30) REVERT: F 76 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.6323 (p0) REVERT: F 117 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7239 (tpp) outliers start: 38 outliers final: 13 residues processed: 149 average time/residue: 1.9556 time to fit residues: 310.9901 Evaluate side-chains 141 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain 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 F residue 2 MET Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.150256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135754 restraints weight = 9611.639| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.31 r_work: 0.3457 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9152 Z= 0.299 Angle : 0.690 11.049 12506 Z= 0.335 Chirality : 0.044 0.221 1463 Planarity : 0.005 0.050 1529 Dihedral : 9.301 85.638 1323 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.99 % Favored : 93.83 % Rotamer: Outliers : 3.49 % Allowed : 16.47 % Favored : 80.04 % 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: 0.71 (0.26), residues: 1118 helix: 1.46 (0.20), residues: 705 sheet: -1.00 (0.73), residues: 50 loop : -1.29 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 55 HIS 0.004 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.011 0.001 TYR F 192 ARG 0.009 0.000 ARG B 71 *********************** 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 157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.005 Fit side-chains REVERT: B 2 MET cc_start: 0.6650 (mtm) cc_final: 0.5486 (tpt) REVERT: B 71 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7822 (ttm-80) REVERT: B 87 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7657 (pt) REVERT: C 86 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6955 (mtt) REVERT: E -1 MET cc_start: 0.5620 (OUTLIER) cc_final: 0.5031 (mpp) REVERT: E 28 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7734 (mm-30) REVERT: F 10 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7618 (mm-30) REVERT: F 117 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7219 (tpp) outliers start: 32 outliers final: 15 residues processed: 138 average time/residue: 1.2171 time to fit residues: 179.5516 Evaluate side-chains 142 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 76 ASP 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 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 E residue 167 GLN Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.152688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138131 restraints weight = 9700.799| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.33 r_work: 0.3496 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.003 0.042 9152 Z= 0.224 Angle : 0.651 11.333 12506 Z= 0.315 Chirality : 0.042 0.245 1463 Planarity : 0.005 0.056 1529 Dihedral : 9.188 87.237 1323 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.17 % Favored : 93.65 % Rotamer: Outliers : 2.73 % Allowed : 17.01 % 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: 0.94 (0.26), residues: 1118 helix: 1.64 (0.20), residues: 707 sheet: -1.04 (0.74), residues: 50 loop : -1.18 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 55 HIS 0.004 0.001 HIS A 73 PHE 0.015 0.001 PHE B 3 TYR 0.010 0.001 TYR F 192 ARG 0.007 0.000 ARG B 71 *********************** 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 150 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.913 Fit side-chains REVERT: B 1 MET cc_start: 0.5351 (mmt) cc_final: 0.5019 (mtt) REVERT: B 2 MET cc_start: 0.6512 (mtm) cc_final: 0.5369 (tpt) REVERT: B 71 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7752 (ttm-80) REVERT: B 87 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7593 (pt) REVERT: C 86 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6874 (mtt) REVERT: E -1 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.4900 (mpp) REVERT: E 28 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7682 (mm-30) REVERT: E 57 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: E 175 GLN cc_start: 0.7092 (pt0) cc_final: 0.6572 (mp10) REVERT: F 10 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7598 (mm-30) REVERT: F 117 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7192 (tpp) outliers start: 25 outliers final: 12 residues processed: 136 average time/residue: 1.1704 time to fit residues: 170.4313 Evaluate side-chains 140 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 76 ASP 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 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 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.153863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139319 restraints weight = 9806.141| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.34 r_work: 0.3499 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9152 Z= 0.208 Angle : 0.637 11.169 12506 Z= 0.308 Chirality : 0.042 0.256 1463 Planarity : 0.005 0.061 1529 Dihedral : 9.093 88.815 1323 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.51 % Allowed : 17.45 % Favored : 80.04 % 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: 706 sheet: -1.03 (0.75), residues: 50 loop : -1.16 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 55 HIS 0.003 0.001 HIS A 73 PHE 0.015 0.001 PHE B 3 TYR 0.010 0.001 TYR F 192 ARG 0.007 0.000 ARG B 71 *********************** 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 146 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.858 Fit side-chains REVERT: B 1 MET cc_start: 0.5355 (mmt) cc_final: 0.5024 (mtt) REVERT: B 2 MET cc_start: 0.6457 (mtm) cc_final: 0.5379 (tpt) REVERT: B 71 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7705 (ttm-80) REVERT: B 87 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7564 (pt) REVERT: C 86 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6829 (mtt) REVERT: E -1 MET cc_start: 0.5454 (OUTLIER) cc_final: 0.4822 (mpp) REVERT: E 28 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7654 (mm-30) REVERT: E 57 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6981 (pm20) REVERT: E 175 GLN cc_start: 0.7039 (pt0) cc_final: 0.6553 (mp10) REVERT: F 1 MET cc_start: 0.6999 (ttp) cc_final: 0.6544 (tmm) REVERT: F 10 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7576 (mm-30) REVERT: F 117 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7226 (tpp) outliers start: 23 outliers final: 9 residues processed: 131 average time/residue: 1.2283 time to fit residues: 171.6989 Evaluate side-chains 131 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139263 restraints weight = 9726.757| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.33 r_work: 0.3499 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9152 Z= 0.215 Angle : 0.634 10.221 12506 Z= 0.307 Chirality : 0.042 0.249 1463 Planarity : 0.005 0.063 1529 Dihedral : 8.958 89.552 1323 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 2.29 % Allowed : 18.32 % 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: 1.08 (0.26), residues: 1118 helix: 1.78 (0.20), residues: 706 sheet: -1.09 (0.75), residues: 50 loop : -1.17 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.007 0.000 ARG B 71 *********************** 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 140 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.844 Fit side-chains REVERT: B 1 MET cc_start: 0.5320 (mmt) cc_final: 0.5036 (mtt) REVERT: B 2 MET cc_start: 0.6452 (mtm) cc_final: 0.5362 (tpt) REVERT: B 71 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7686 (ttm-80) REVERT: B 87 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7576 (pt) REVERT: C 86 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6799 (mtt) REVERT: E -1 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.4901 (mpp) REVERT: E 28 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7642 (mm-30) REVERT: E 57 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: E 175 GLN cc_start: 0.7055 (pt0) cc_final: 0.6550 (mp10) REVERT: F 1 MET cc_start: 0.6963 (ttp) cc_final: 0.6549 (tmm) REVERT: F 10 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 117 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7241 (tpp) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 1.3616 time to fit residues: 183.9495 Evaluate side-chains 134 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 C residue 183 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 58 optimal weight: 0.0060 chunk 67 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS D 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141399 restraints weight = 9697.706| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.33 r_work: 0.3539 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9152 Z= 0.172 Angle : 0.621 8.803 12506 Z= 0.299 Chirality : 0.041 0.248 1463 Planarity : 0.005 0.063 1529 Dihedral : 8.862 88.678 1323 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 1.64 % Allowed : 18.97 % 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: 1.18 (0.26), residues: 1118 helix: 1.89 (0.20), residues: 704 sheet: -1.09 (0.76), residues: 50 loop : -1.17 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 55 HIS 0.005 0.001 HIS C 184 PHE 0.015 0.001 PHE B 3 TYR 0.009 0.001 TYR F 192 ARG 0.007 0.000 ARG E 196 ********************** 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 139 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.964 Fit side-chains REVERT: B 1 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.4945 (mtp) REVERT: B 2 MET cc_start: 0.6335 (mtm) cc_final: 0.5263 (tpt) REVERT: B 71 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7673 (ttm-80) REVERT: B 87 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7490 (pt) REVERT: B 124 TYR cc_start: 0.8043 (t80) cc_final: 0.7804 (t80) REVERT: C 21 PHE cc_start: 0.7319 (m-80) cc_final: 0.6942 (m-80) REVERT: C 86 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6821 (mtt) REVERT: E -1 MET cc_start: 0.5449 (OUTLIER) cc_final: 0.4745 (mpp) REVERT: E 1 MET cc_start: 0.8189 (mmt) cc_final: 0.7515 (mmm) REVERT: E 28 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7589 (mm-30) REVERT: E 57 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: E 175 GLN cc_start: 0.7065 (pt0) cc_final: 0.6574 (mp10) REVERT: F 1 MET cc_start: 0.6963 (ttp) cc_final: 0.6554 (tmm) REVERT: F 10 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7550 (mm-30) REVERT: F 117 MET cc_start: 0.7630 (mtp) cc_final: 0.7221 (tpp) outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 1.7031 time to fit residues: 239.0950 Evaluate side-chains 133 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140056 restraints weight = 9685.538| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.33 r_work: 0.3507 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9152 Z= 0.215 Angle : 0.638 10.994 12506 Z= 0.307 Chirality : 0.042 0.249 1463 Planarity : 0.005 0.059 1529 Dihedral : 8.825 88.296 1323 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 1.85 % Allowed : 19.08 % Favored : 79.06 % 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: 1.17 (0.26), residues: 1118 helix: 1.86 (0.20), residues: 706 sheet: -1.06 (0.76), residues: 50 loop : -1.14 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 0.007 0.000 ARG E 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6227.57 seconds wall clock time: 110 minutes 3.17 seconds (6603.17 seconds total)