Starting phenix.real_space_refine on Mon Aug 25 22:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j05_35884/08_2025/8j05_35884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j05_35884/08_2025/8j05_35884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j05_35884/08_2025/8j05_35884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j05_35884/08_2025/8j05_35884_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j05_35884/08_2025/8j05_35884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j05_35884/08_2025/8j05_35884.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 10208 2.51 5 N 2708 2.21 5 O 2872 1.98 5 H 15800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31676 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "C" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "E" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5741 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 6, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Time building chain proxies: 4.91, per 1000 atoms: 0.16 Number of scatterers: 31676 At special positions: 0 Unit cell: (126.48, 127.41, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 O 2872 8.00 N 2708 7.00 C 10208 6.00 H 15800 1.00 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=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 760.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 4 sheets defined 81.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 4.124A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.729A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 166 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 329 removed outlier: 3.900A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 538 through 558 Processing helix chain 'A' and resid 562 through 595 removed outlier: 4.604A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 115 removed outlier: 4.096A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.717A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.620A pdb=" N LYS B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.961A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 329 removed outlier: 3.946A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 538 through 559 Processing helix chain 'B' and resid 564 through 595 Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.787A pdb=" N THR C 80 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.832A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 115 removed outlier: 4.074A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.703A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 329 removed outlier: 3.998A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 332 through 350 Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 538 through 558 Processing helix chain 'D' and resid 564 through 595 Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 74 Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.988A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.094A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 146 removed outlier: 3.525A pdb=" N MET F 146 " --> pdb=" O PHE F 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 115 removed outlier: 4.124A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 3.705A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.673A pdb=" N MET G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 255 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 329 removed outlier: 3.858A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix Processing helix chain 'G' and resid 332 through 350 Processing helix chain 'G' and resid 357 through 367 removed outlier: 3.528A pdb=" N VAL G 367 " --> pdb=" O TYR G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 558 Processing helix chain 'G' and resid 564 through 595 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.879A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 148 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 removed outlier: 3.575A pdb=" N ILE F 101 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 137 " --> pdb=" O ILE F 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102 1189 hydrogen bonds defined for protein. 3549 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: 6.70 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15772 1.03 - 1.23: 28 1.23 - 1.42: 7000 1.42 - 1.62: 9060 1.62 - 1.81: 148 Bond restraints: 32008 Sorted by residual: bond pdb=" C ARG G 87 " pdb=" N PRO G 88 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.23e-02 6.61e+03 8.82e-01 bond pdb=" CB GLU D 123 " pdb=" CG GLU D 123 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.40e-01 bond pdb=" CB ILE D 205 " pdb=" CG2 ILE D 205 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.63e-01 bond pdb=" CB GLN D 78 " pdb=" CG GLN D 78 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 5.83e-01 bond pdb=" CB VAL G 320 " pdb=" CG1 VAL G 320 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.25e-01 ... (remaining 32003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 55712 1.27 - 2.54: 1760 2.54 - 3.81: 80 3.81 - 5.08: 28 5.08 - 6.35: 4 Bond angle restraints: 57584 Sorted by residual: angle pdb=" N ARG D 213 " pdb=" CA ARG D 213 " pdb=" CB ARG D 213 " ideal model delta sigma weight residual 113.65 110.16 3.49 1.47e+00 4.63e-01 5.62e+00 angle pdb=" CB GLU D 123 " pdb=" CG GLU D 123 " pdb=" CD GLU D 123 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.70e+00 3.46e-01 5.22e+00 angle pdb=" N GLY D 256 " pdb=" CA GLY D 256 " pdb=" C GLY D 256 " ideal model delta sigma weight residual 112.49 115.23 -2.74 1.21e+00 6.83e-01 5.13e+00 angle pdb=" CA TYR G 571 " pdb=" CB TYR G 571 " pdb=" CG TYR G 571 " ideal model delta sigma weight residual 113.90 109.90 4.00 1.80e+00 3.09e-01 4.93e+00 angle pdb=" C ASP F 65 " pdb=" N PHE F 66 " pdb=" CA PHE F 66 " ideal model delta sigma weight residual 119.78 122.50 -2.72 1.24e+00 6.50e-01 4.83e+00 ... (remaining 57579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13113 17.83 - 35.66: 1209 35.66 - 53.49: 459 53.49 - 71.32: 115 71.32 - 89.15: 20 Dihedral angle restraints: 14916 sinusoidal: 7960 harmonic: 6956 Sorted by residual: dihedral pdb=" CA ASP C 57 " pdb=" CB ASP C 57 " pdb=" CG ASP C 57 " pdb=" OD1 ASP C 57 " ideal model delta sinusoidal sigma weight residual -30.00 -89.82 59.82 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG D 89 " pdb=" CD ARG D 89 " pdb=" NE ARG D 89 " pdb=" CZ ARG D 89 " ideal model delta sinusoidal sigma weight residual -90.00 -134.95 44.95 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU E 121 " pdb=" CG GLU E 121 " pdb=" CD GLU E 121 " pdb=" OE1 GLU E 121 " ideal model delta sinusoidal sigma weight residual 0.00 89.15 -89.15 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 14913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1593 0.027 - 0.053: 530 0.053 - 0.080: 196 0.080 - 0.106: 58 0.106 - 0.133: 19 Chirality restraints: 2396 Sorted by residual: chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE F 64 " pdb=" N ILE F 64 " pdb=" C ILE F 64 " pdb=" CB ILE F 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2393 not shown) Planarity restraints: 4672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 123 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" CD GLU D 123 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU D 123 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 123 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 101 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C LEU D 101 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU D 101 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU D 102 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 100 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C PHE D 100 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE D 100 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU D 101 " 0.008 2.00e-02 2.50e+03 ... (remaining 4669 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1875 2.18 - 2.79: 64647 2.79 - 3.39: 92053 3.39 - 4.00: 112504 4.00 - 4.60: 176612 Nonbonded interactions: 447691 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" HH TYR D 280 " model vdw 1.578 2.450 nonbonded pdb=" OD1 ASP C 57 " pdb=" H GLY C 60 " model vdw 1.580 2.450 nonbonded pdb=" OE2 GLU D 140 " pdb="HH22 ARG D 210 " model vdw 1.590 2.450 nonbonded pdb=" HH TYR A 95 " pdb=" OE1 GLU A 140 " model vdw 1.598 2.450 nonbonded pdb=" O LEU B 272 " pdb=" HG1 THR B 276 " model vdw 1.606 2.450 ... (remaining 447686 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 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } 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: 0.860 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.430 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 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 : 0.003 0.028 16208 Z= 0.127 Angle : 0.470 6.347 21860 Z= 0.264 Chirality : 0.033 0.133 2396 Planarity : 0.003 0.029 2760 Dihedral : 17.085 89.151 5916 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.84 % Allowed : 25.89 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.19), residues: 1928 helix: 1.89 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.04 (0.35), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 325 TYR 0.019 0.001 TYR G 571 PHE 0.015 0.001 PHE E 90 TRP 0.014 0.001 TRP B 344 HIS 0.006 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00267 (16208) covalent geometry : angle 0.47017 (21860) hydrogen bonds : bond 0.10623 ( 1189) hydrogen bonds : angle 5.37227 ( 3549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.3614 (ppp) cc_final: 0.3247 (ptp) REVERT: B 130 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 166 LYS cc_start: 0.7267 (ttpp) cc_final: 0.6826 (tttm) REVERT: C 72 MET cc_start: -0.1029 (tpt) cc_final: -0.1242 (tpt) REVERT: C 73 MET cc_start: 0.0966 (mmp) cc_final: -0.2878 (tpt) REVERT: C 146 MET cc_start: 0.5845 (tmm) cc_final: 0.5028 (tpt) REVERT: D 87 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7369 (pmt-80) REVERT: D 127 TYR cc_start: 0.7906 (t80) cc_final: 0.7575 (t80) REVERT: D 158 ARG cc_start: 0.6947 (tpt170) cc_final: 0.6552 (mmp80) REVERT: F 146 MET cc_start: 0.3587 (tpp) cc_final: 0.3287 (tpp) REVERT: G 158 ARG cc_start: 0.6848 (tpt170) cc_final: 0.6504 (mmp80) outliers start: 14 outliers final: 11 residues processed: 180 average time/residue: 0.8979 time to fit residues: 185.3747 Evaluate side-chains 156 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain H residue 77 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 341 GLN B 341 GLN D 204 GLN G 79 ASN ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.253439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.149022 restraints weight = 55640.293| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.72 r_work: 0.3512 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16208 Z= 0.221 Angle : 0.525 5.379 21860 Z= 0.295 Chirality : 0.036 0.133 2396 Planarity : 0.004 0.055 2760 Dihedral : 4.352 46.939 2195 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.39 % Allowed : 24.46 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.19), residues: 1928 helix: 1.99 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : 0.09 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 581 TYR 0.017 0.002 TYR G 571 PHE 0.022 0.001 PHE E 90 TRP 0.011 0.001 TRP B 344 HIS 0.013 0.001 HIS G 328 Details of bonding type rmsd covalent geometry : bond 0.00497 (16208) covalent geometry : angle 0.52451 (21860) hydrogen bonds : bond 0.04343 ( 1189) hydrogen bonds : angle 4.52854 ( 3549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6330 (t80) REVERT: A 208 MET cc_start: 0.7244 (tpt) cc_final: 0.7003 (mmm) REVERT: A 565 MET cc_start: 0.3374 (ppp) cc_final: 0.2969 (ptp) REVERT: C 72 MET cc_start: -0.1243 (tpt) cc_final: -0.1444 (tpt) REVERT: C 73 MET cc_start: 0.0735 (mmp) cc_final: -0.2967 (tpt) REVERT: D 127 TYR cc_start: 0.8041 (t80) cc_final: 0.7718 (t80) REVERT: D 208 MET cc_start: 0.7064 (tpt) cc_final: 0.6855 (mmm) REVERT: D 289 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8125 (m110) REVERT: E 124 GLU cc_start: -0.0936 (tm-30) cc_final: -0.1279 (tm-30) REVERT: F 84 GLU cc_start: 0.6583 (tt0) cc_final: 0.5573 (mp0) REVERT: F 146 MET cc_start: 0.3765 (tpp) cc_final: 0.3554 (tpp) REVERT: G 158 ARG cc_start: 0.7246 (tpt170) cc_final: 0.6878 (mmm160) outliers start: 40 outliers final: 21 residues processed: 169 average time/residue: 0.9301 time to fit residues: 179.4362 Evaluate side-chains 163 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 79 ASN B 341 GLN D 204 GLN G 328 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.255073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151877 restraints weight = 55685.233| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.66 r_work: 0.3438 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16208 Z= 0.141 Angle : 0.477 5.856 21860 Z= 0.265 Chirality : 0.033 0.128 2396 Planarity : 0.003 0.045 2760 Dihedral : 3.719 29.853 2174 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.68 % Allowed : 23.69 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.19), residues: 1928 helix: 2.15 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.00 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 91 TYR 0.019 0.001 TYR G 571 PHE 0.016 0.001 PHE E 90 TRP 0.010 0.001 TRP B 344 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00305 (16208) covalent geometry : angle 0.47694 (21860) hydrogen bonds : bond 0.03851 ( 1189) hydrogen bonds : angle 4.27702 ( 3549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7649 (tptm) REVERT: A 168 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6164 (t80) REVERT: A 289 ASN cc_start: 0.8378 (m110) cc_final: 0.8087 (m110) REVERT: A 565 MET cc_start: 0.3834 (ppp) cc_final: 0.3413 (ptp) REVERT: B 166 LYS cc_start: 0.6938 (ttpp) cc_final: 0.6486 (tttm) REVERT: C 72 MET cc_start: -0.1378 (tpt) cc_final: -0.1607 (tpt) REVERT: C 73 MET cc_start: 0.0678 (mmp) cc_final: -0.3217 (tpt) REVERT: D 127 TYR cc_start: 0.8003 (t80) cc_final: 0.7656 (t80) REVERT: D 168 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.6197 (t80) REVERT: D 197 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5579 (pp) REVERT: E 110 MET cc_start: 0.2116 (mmp) cc_final: 0.1867 (mmp) REVERT: F 84 GLU cc_start: 0.6545 (tt0) cc_final: 0.5575 (mp0) REVERT: F 146 MET cc_start: 0.4202 (tpp) cc_final: 0.3909 (tpp) REVERT: G 158 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6841 (mmm160) REVERT: G 229 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8910 (p) outliers start: 45 outliers final: 22 residues processed: 176 average time/residue: 0.9675 time to fit residues: 195.5644 Evaluate side-chains 169 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 341 GLN D 204 GLN G 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.254774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147310 restraints weight = 54763.594| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.38 r_work: 0.3392 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16208 Z= 0.196 Angle : 0.501 5.257 21860 Z= 0.280 Chirality : 0.035 0.128 2396 Planarity : 0.003 0.042 2760 Dihedral : 3.794 29.988 2174 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.40 % Allowed : 23.39 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.19), residues: 1928 helix: 2.06 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.01 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 581 TYR 0.019 0.002 TYR G 571 PHE 0.022 0.001 PHE E 20 TRP 0.011 0.001 TRP B 344 HIS 0.011 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00439 (16208) covalent geometry : angle 0.50080 (21860) hydrogen bonds : bond 0.03948 ( 1189) hydrogen bonds : angle 4.29090 ( 3549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7652 (tptm) REVERT: A 168 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6389 (t80) REVERT: A 289 ASN cc_start: 0.8533 (m110) cc_final: 0.8064 (m110) REVERT: A 565 MET cc_start: 0.3817 (ppp) cc_final: 0.3450 (ptp) REVERT: B 130 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7893 (mt-10) REVERT: B 166 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6501 (tttm) REVERT: C 146 MET cc_start: 0.5684 (tmm) cc_final: 0.4703 (tpt) REVERT: D 127 TYR cc_start: 0.7947 (t80) cc_final: 0.7662 (t80) REVERT: D 197 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5609 (pp) REVERT: D 289 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: E 82 SER cc_start: 0.2996 (OUTLIER) cc_final: 0.2601 (t) REVERT: E 88 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6771 (mm-30) REVERT: F 84 GLU cc_start: 0.6513 (tt0) cc_final: 0.5521 (mp0) REVERT: F 146 MET cc_start: 0.4215 (tpp) cc_final: 0.3839 (tpp) REVERT: G 133 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7829 (t) REVERT: G 158 ARG cc_start: 0.7109 (tpt170) cc_final: 0.6771 (mmm160) REVERT: G 229 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8899 (p) outliers start: 57 outliers final: 34 residues processed: 175 average time/residue: 1.0455 time to fit residues: 207.5292 Evaluate side-chains 178 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 341 GLN D 204 GLN G 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.254263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145944 restraints weight = 54918.304| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.28 r_work: 0.3396 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16208 Z= 0.217 Angle : 0.514 5.844 21860 Z= 0.287 Chirality : 0.036 0.130 2396 Planarity : 0.003 0.038 2760 Dihedral : 3.814 18.399 2172 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.76 % Allowed : 23.45 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.19), residues: 1928 helix: 1.93 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.07 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.020 0.002 TYR G 571 PHE 0.021 0.001 PHE E 20 TRP 0.011 0.001 TRP D 157 HIS 0.011 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00490 (16208) covalent geometry : angle 0.51357 (21860) hydrogen bonds : bond 0.03995 ( 1189) hydrogen bonds : angle 4.31521 ( 3549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7675 (tptm) REVERT: A 158 ARG cc_start: 0.6715 (tpm-80) cc_final: 0.6452 (mmm160) REVERT: A 168 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6372 (t80) REVERT: A 289 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8078 (m110) REVERT: A 565 MET cc_start: 0.3889 (ppp) cc_final: 0.3528 (ptp) REVERT: B 166 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6507 (tttm) REVERT: C 146 MET cc_start: 0.5576 (tmm) cc_final: 0.4601 (tpt) REVERT: D 127 TYR cc_start: 0.7988 (t80) cc_final: 0.7666 (t80) REVERT: D 197 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5642 (pp) REVERT: D 289 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: D 560 ARG cc_start: 0.4680 (OUTLIER) cc_final: 0.4397 (mtm-85) REVERT: E 88 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6831 (mm-30) REVERT: F 73 MET cc_start: 0.0609 (OUTLIER) cc_final: -0.1768 (ttt) REVERT: F 84 GLU cc_start: 0.6655 (tt0) cc_final: 0.5693 (mp0) REVERT: F 146 MET cc_start: 0.4204 (tpp) cc_final: 0.3865 (tpp) REVERT: G 133 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7876 (t) REVERT: G 158 ARG cc_start: 0.7087 (tpt170) cc_final: 0.6761 (mmm160) REVERT: G 208 MET cc_start: 0.7005 (tpt) cc_final: 0.6763 (mmm) outliers start: 63 outliers final: 39 residues processed: 181 average time/residue: 1.1397 time to fit residues: 234.0525 Evaluate side-chains 182 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 5.9990 chunk 187 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN G 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.255708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.150918 restraints weight = 54736.738| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.36 r_work: 0.3398 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16208 Z= 0.130 Angle : 0.481 6.154 21860 Z= 0.266 Chirality : 0.033 0.129 2396 Planarity : 0.003 0.038 2760 Dihedral : 3.700 17.313 2172 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.16 % Allowed : 23.99 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.19), residues: 1928 helix: 2.14 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.14 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 207 TYR 0.019 0.001 TYR D 571 PHE 0.017 0.001 PHE E 20 TRP 0.011 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00283 (16208) covalent geometry : angle 0.48104 (21860) hydrogen bonds : bond 0.03624 ( 1189) hydrogen bonds : angle 4.14747 ( 3549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7610 (tptm) REVERT: A 158 ARG cc_start: 0.6705 (tpm-80) cc_final: 0.6408 (mmm160) REVERT: A 168 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6350 (t80) REVERT: A 289 ASN cc_start: 0.8430 (m110) cc_final: 0.8050 (m-40) REVERT: A 565 MET cc_start: 0.3816 (ppp) cc_final: 0.3529 (ptp) REVERT: B 123 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: B 130 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 166 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6430 (tttm) REVERT: C 73 MET cc_start: 0.0714 (mmp) cc_final: -0.2696 (tpt) REVERT: C 146 MET cc_start: 0.5740 (tmm) cc_final: 0.4694 (tpt) REVERT: D 127 TYR cc_start: 0.7899 (t80) cc_final: 0.7538 (t80) REVERT: D 157 TRP cc_start: 0.5593 (m100) cc_final: 0.5173 (m100) REVERT: D 197 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5663 (pp) REVERT: D 560 ARG cc_start: 0.4664 (OUTLIER) cc_final: 0.4428 (mtm-85) REVERT: E 82 SER cc_start: 0.3032 (OUTLIER) cc_final: 0.2602 (t) REVERT: E 88 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6729 (mm-30) REVERT: F 84 GLU cc_start: 0.6529 (tt0) cc_final: 0.5557 (mp0) REVERT: F 146 MET cc_start: 0.4231 (tpp) cc_final: 0.3907 (tpp) REVERT: G 120 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7551 (tptm) REVERT: G 133 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7837 (t) REVERT: G 158 ARG cc_start: 0.7092 (tpt170) cc_final: 0.6773 (mmm160) outliers start: 53 outliers final: 37 residues processed: 173 average time/residue: 1.0976 time to fit residues: 215.6204 Evaluate side-chains 182 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 171 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 overall best weight: 6.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN B 341 GLN D 204 GLN G 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.251521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.155502 restraints weight = 55676.828| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.84 r_work: 0.3393 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.087 16208 Z= 0.432 Angle : 0.645 7.086 21860 Z= 0.362 Chirality : 0.046 0.196 2396 Planarity : 0.005 0.055 2760 Dihedral : 4.219 19.690 2172 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.12 % Allowed : 23.99 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 1928 helix: 1.26 (0.12), residues: 1536 sheet: None (None), residues: 0 loop : -0.31 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 291 TYR 0.034 0.003 TYR A 74 PHE 0.022 0.002 PHE A 168 TRP 0.011 0.003 TRP A 157 HIS 0.013 0.002 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00996 (16208) covalent geometry : angle 0.64500 (21860) hydrogen bonds : bond 0.04938 ( 1189) hydrogen bonds : angle 4.69098 ( 3549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 133 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7869 (tptm) REVERT: A 133 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8024 (t) REVERT: A 168 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 565 MET cc_start: 0.3642 (ppp) cc_final: 0.3303 (ptp) REVERT: B 130 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 133 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8030 (t) REVERT: B 166 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6829 (tttm) REVERT: D 127 TYR cc_start: 0.8077 (t80) cc_final: 0.7761 (t80) REVERT: D 197 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5717 (pp) REVERT: D 327 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7667 (pptt) REVERT: D 560 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.4492 (mtm-85) REVERT: E 88 GLU cc_start: 0.7235 (mm-30) cc_final: 0.7010 (mm-30) REVERT: F 73 MET cc_start: -0.0049 (OUTLIER) cc_final: -0.2124 (ttt) REVERT: F 84 GLU cc_start: 0.6966 (tt0) cc_final: 0.5854 (mp0) REVERT: F 146 MET cc_start: 0.4236 (tpp) cc_final: 0.3921 (tpp) REVERT: G 70 ARG cc_start: 0.4550 (ptt90) cc_final: 0.4290 (ptm-80) REVERT: G 120 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7851 (tptm) REVERT: G 133 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7962 (t) REVERT: G 208 MET cc_start: 0.7299 (tpt) cc_final: 0.7090 (mmm) REVERT: H 52 MET cc_start: -0.1454 (OUTLIER) cc_final: -0.3164 (ttp) outliers start: 69 outliers final: 42 residues processed: 185 average time/residue: 1.0413 time to fit residues: 217.8944 Evaluate side-chains 186 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 341 GLN G 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.255386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150281 restraints weight = 54748.323| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.10 r_work: 0.3403 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16208 Z= 0.126 Angle : 0.500 6.312 21860 Z= 0.276 Chirality : 0.033 0.130 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.834 17.357 2172 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.86 % Allowed : 25.95 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 1928 helix: 1.90 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.22 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 201 TYR 0.020 0.001 TYR D 571 PHE 0.019 0.001 PHE E 90 TRP 0.016 0.001 TRP B 344 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00272 (16208) covalent geometry : angle 0.50039 (21860) hydrogen bonds : bond 0.03697 ( 1189) hydrogen bonds : angle 4.21505 ( 3549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7629 (tptm) REVERT: A 133 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7826 (t) REVERT: A 168 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6347 (t80) REVERT: A 289 ASN cc_start: 0.8470 (m110) cc_final: 0.8100 (m-40) REVERT: A 565 MET cc_start: 0.3928 (ppp) cc_final: 0.3550 (ptp) REVERT: B 166 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6546 (tttm) REVERT: B 197 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5688 (pp) REVERT: C 146 MET cc_start: 0.5795 (tmm) cc_final: 0.4813 (tpt) REVERT: D 127 TYR cc_start: 0.7945 (t80) cc_final: 0.7593 (t80) REVERT: D 157 TRP cc_start: 0.5563 (m100) cc_final: 0.5160 (m100) REVERT: D 197 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5704 (pp) REVERT: D 327 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7415 (pptt) REVERT: D 560 ARG cc_start: 0.4823 (OUTLIER) cc_final: 0.4578 (mtm-85) REVERT: E 88 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6834 (mm-30) REVERT: F 73 MET cc_start: 0.0439 (OUTLIER) cc_final: -0.1859 (ttt) REVERT: F 84 GLU cc_start: 0.6720 (tt0) cc_final: 0.5752 (mp0) REVERT: F 146 MET cc_start: 0.4066 (tpp) cc_final: 0.3691 (tpp) REVERT: G 70 ARG cc_start: 0.4277 (ptt90) cc_final: 0.4017 (ptm-80) REVERT: G 120 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7549 (tptm) REVERT: G 123 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7164 (mt-10) REVERT: G 133 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7850 (t) outliers start: 48 outliers final: 31 residues processed: 172 average time/residue: 1.0573 time to fit residues: 207.3406 Evaluate side-chains 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 145 optimal weight: 0.0980 chunk 74 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN G 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.252784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145458 restraints weight = 54508.228| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.86 r_work: 0.3369 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16208 Z= 0.265 Angle : 0.551 6.760 21860 Z= 0.306 Chirality : 0.038 0.150 2396 Planarity : 0.004 0.079 2760 Dihedral : 3.982 17.937 2172 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.10 % Allowed : 26.19 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.19), residues: 1928 helix: 1.71 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 291 TYR 0.022 0.002 TYR A 74 PHE 0.019 0.002 PHE E 90 TRP 0.013 0.002 TRP B 344 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00600 (16208) covalent geometry : angle 0.55066 (21860) hydrogen bonds : bond 0.04189 ( 1189) hydrogen bonds : angle 4.39096 ( 3549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7691 (tptm) REVERT: A 133 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7867 (t) REVERT: A 168 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6468 (t80) REVERT: A 289 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.7903 (m110) REVERT: A 565 MET cc_start: 0.4052 (ppp) cc_final: 0.3748 (ptp) REVERT: B 130 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 166 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6606 (tttm) REVERT: B 197 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5657 (pp) REVERT: C 146 MET cc_start: 0.5776 (tmm) cc_final: 0.4800 (tpt) REVERT: D 127 TYR cc_start: 0.7953 (t80) cc_final: 0.7604 (t80) REVERT: D 157 TRP cc_start: 0.5525 (m100) cc_final: 0.5136 (m100) REVERT: D 197 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5743 (pp) REVERT: D 560 ARG cc_start: 0.4862 (OUTLIER) cc_final: 0.4585 (mtm-85) REVERT: E 88 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6905 (mm-30) REVERT: F 73 MET cc_start: 0.0270 (OUTLIER) cc_final: -0.1827 (ttt) REVERT: F 77 MET cc_start: 0.0084 (OUTLIER) cc_final: -0.0599 (pp-130) REVERT: F 84 GLU cc_start: 0.6706 (tt0) cc_final: 0.5774 (mp0) REVERT: G 70 ARG cc_start: 0.4277 (ptt90) cc_final: 0.4038 (ptm-80) REVERT: G 120 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7651 (tptm) REVERT: G 133 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7838 (t) outliers start: 52 outliers final: 37 residues processed: 165 average time/residue: 1.0288 time to fit residues: 193.3354 Evaluate side-chains 181 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 76 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN G 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.255073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149222 restraints weight = 54638.469| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.10 r_work: 0.3398 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16208 Z= 0.136 Angle : 0.498 6.619 21860 Z= 0.275 Chirality : 0.033 0.129 2396 Planarity : 0.003 0.070 2760 Dihedral : 3.806 17.066 2172 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.51 % Allowed : 26.91 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.19), residues: 1928 helix: 2.01 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.020 0.001 TYR D 571 PHE 0.019 0.001 PHE E 90 TRP 0.015 0.001 TRP B 344 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00298 (16208) covalent geometry : angle 0.49818 (21860) hydrogen bonds : bond 0.03642 ( 1189) hydrogen bonds : angle 4.17604 ( 3549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7650 (tptm) REVERT: A 133 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7860 (t) REVERT: A 168 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6476 (t80) REVERT: A 289 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: A 565 MET cc_start: 0.4052 (ppp) cc_final: 0.3764 (ptp) REVERT: B 166 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6568 (tttm) REVERT: C 146 MET cc_start: 0.5790 (tmm) cc_final: 0.4808 (tpt) REVERT: D 127 TYR cc_start: 0.7961 (t80) cc_final: 0.7613 (t80) REVERT: D 157 TRP cc_start: 0.5523 (m100) cc_final: 0.5111 (m100) REVERT: D 197 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5749 (pp) REVERT: E 88 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6729 (mm-30) REVERT: F 84 GLU cc_start: 0.6731 (tt0) cc_final: 0.5735 (mp0) REVERT: G 70 ARG cc_start: 0.4351 (ptt90) cc_final: 0.4090 (ptm-80) REVERT: G 120 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7565 (tptm) REVERT: G 123 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7174 (mt-10) REVERT: G 133 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7848 (t) outliers start: 42 outliers final: 32 residues processed: 165 average time/residue: 1.1309 time to fit residues: 211.5405 Evaluate side-chains 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN B 341 GLN G 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.255198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149598 restraints weight = 54797.124| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.21 r_work: 0.3364 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16208 Z= 0.242 Angle : 0.546 8.605 21860 Z= 0.303 Chirality : 0.037 0.143 2396 Planarity : 0.004 0.072 2760 Dihedral : 3.946 18.056 2172 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.98 % Allowed : 26.73 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.19), residues: 1928 helix: 1.81 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.16 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 291 TYR 0.021 0.002 TYR A 74 PHE 0.019 0.002 PHE E 90 TRP 0.014 0.002 TRP B 344 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00547 (16208) covalent geometry : angle 0.54600 (21860) hydrogen bonds : bond 0.04067 ( 1189) hydrogen bonds : angle 4.32860 ( 3549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16022.05 seconds wall clock time: 270 minutes 46.16 seconds (16246.16 seconds total)