Starting phenix.real_space_refine on Fri Jun 27 05:30:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j05_35884/06_2025/8j05_35884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j05_35884/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j05_35884/06_2025/8j05_35884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j05_35884/06_2025/8j05_35884.map" model { file = "/net/cci-nas-00/data/ceres_data/8j05_35884/06_2025/8j05_35884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j05_35884/06_2025/8j05_35884_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.64, per 1000 atoms: 0.49 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: 9.66 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.76 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: 12.33 Time building geometry restraints manager: 10.75 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: 0.01 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.570 Extract box with map and model: 1.410 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 68.400 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP B 344 HIS 0.006 0.001 HIS A 575 PHE 0.015 0.001 PHE E 90 TYR 0.019 0.001 TYR G 571 ARG 0.002 0.000 ARG G 325 Details of bonding type rmsd hydrogen bonds : bond 0.10623 ( 1189) hydrogen bonds : angle 5.37227 ( 3549) covalent geometry : bond 0.00267 (16208) covalent geometry : angle 0.47017 (21860) *********************** 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 : 2.691 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 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: C 72 MET cc_start: -0.1029 (tpt) cc_final: -0.1245 (tpt) REVERT: C 73 MET cc_start: 0.0966 (mmp) cc_final: -0.2881 (tpt) REVERT: C 146 MET cc_start: 0.5845 (tmm) cc_final: 0.4997 (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 73 MET cc_start: 0.0043 (mmt) cc_final: -0.2294 (ttt) 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: 2.0843 time to fit residues: 434.7640 Evaluate side-chains 157 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 162 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.4826 r_free = 0.4826 target = 0.254447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156234 restraints weight = 55336.357| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.55 r_work: 0.3457 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16208 Z= 0.179 Angle : 0.502 5.425 21860 Z= 0.282 Chirality : 0.034 0.128 2396 Planarity : 0.004 0.054 2760 Dihedral : 4.266 46.962 2195 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.91 % Allowed : 24.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.19), residues: 1928 helix: 2.10 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : 0.09 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.012 0.001 HIS G 328 PHE 0.022 0.001 PHE E 90 TYR 0.017 0.002 TYR G 571 ARG 0.002 0.000 ARG G 560 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1189) hydrogen bonds : angle 4.45997 ( 3549) covalent geometry : bond 0.00395 (16208) covalent geometry : angle 0.50218 (21860) *********************** 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 184 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 2.502 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: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6187 (t80) REVERT: A 208 MET cc_start: 0.7200 (tpt) cc_final: 0.6993 (mmm) REVERT: A 565 MET cc_start: 0.3456 (ppp) cc_final: 0.3045 (ptp) REVERT: B 166 LYS cc_start: 0.7072 (ttpp) cc_final: 0.6648 (tttm) REVERT: C 72 MET cc_start: -0.1281 (tpt) cc_final: -0.1492 (tpt) REVERT: C 73 MET cc_start: 0.0730 (mmp) cc_final: -0.2990 (tpt) REVERT: C 146 MET cc_start: 0.5754 (tmm) cc_final: 0.4906 (tpt) REVERT: D 127 TYR cc_start: 0.8079 (t80) cc_final: 0.7756 (t80) REVERT: D 289 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8181 (m-40) REVERT: E 124 GLU cc_start: -0.0730 (tm-30) cc_final: -0.1097 (tm-30) REVERT: F 84 GLU cc_start: 0.6579 (tt0) cc_final: 0.5584 (mp0) REVERT: F 146 MET cc_start: 0.3800 (tpp) cc_final: 0.3507 (tpp) REVERT: G 158 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6884 (mmm160) outliers start: 32 outliers final: 18 residues processed: 166 average time/residue: 2.2386 time to fit residues: 424.2165 Evaluate side-chains 163 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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 110 SER Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 289 ASN 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 172 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 152 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- 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 = 0.4788 r_free = 0.4788 target = 0.250120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146051 restraints weight = 55757.263| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.40 r_work: 0.3367 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1844 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= 0.435 Angle : 0.653 6.905 21860 Z= 0.369 Chirality : 0.046 0.184 2396 Planarity : 0.005 0.054 2760 Dihedral : 4.326 31.967 2174 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.01 % Allowed : 23.33 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1928 helix: 1.18 (0.12), residues: 1536 sheet: None (None), residues: 0 loop : -0.12 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 157 HIS 0.010 0.002 HIS A 328 PHE 0.022 0.002 PHE D 168 TYR 0.031 0.003 TYR A 74 ARG 0.007 0.001 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 1189) hydrogen bonds : angle 4.89519 ( 3549) covalent geometry : bond 0.01006 (16208) covalent geometry : angle 0.65261 (21860) *********************** 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 216 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 132 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7836 (tptm) REVERT: A 158 ARG cc_start: 0.6866 (tpm-80) cc_final: 0.6508 (mmp80) REVERT: A 565 MET cc_start: 0.3694 (ppp) cc_final: 0.3356 (ptp) REVERT: C 72 MET cc_start: -0.1098 (tpt) cc_final: -0.1462 (tpt) REVERT: D 127 TYR cc_start: 0.8042 (t80) cc_final: 0.7750 (t80) REVERT: D 197 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5739 (pp) REVERT: D 560 ARG cc_start: 0.4879 (OUTLIER) cc_final: 0.4513 (mtm-85) REVERT: F 73 MET cc_start: 0.0316 (mmt) cc_final: -0.1859 (ttt) REVERT: F 84 GLU cc_start: 0.6788 (tt0) cc_final: 0.5834 (mp0) REVERT: F 146 MET cc_start: 0.4258 (tpp) cc_final: 0.4029 (tpp) REVERT: G 133 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7910 (t) REVERT: G 208 MET cc_start: 0.7253 (tpt) cc_final: 0.7044 (mmm) outliers start: 84 outliers final: 46 residues processed: 200 average time/residue: 1.9433 time to fit residues: 448.0502 Evaluate side-chains 178 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LYS 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 204 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 150 CYS 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 296 THR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain C residue 63 THR 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 197 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 296 THR 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 G residue 84 VAL 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 262 ASP Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 296 THR 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 102 SER Chi-restraints excluded: chain H residue 144 GLN 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 47 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 40.0000 chunk 67 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 350 ASN 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 = 0.4834 r_free = 0.4834 target = 0.256024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149977 restraints weight = 54957.222| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.38 r_work: 0.3439 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16208 Z= 0.117 Angle : 0.493 6.239 21860 Z= 0.273 Chirality : 0.033 0.129 2396 Planarity : 0.003 0.038 2760 Dihedral : 3.904 30.261 2174 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.74 % Allowed : 24.64 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 1928 helix: 1.82 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.07 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.011 0.001 HIS A 328 PHE 0.012 0.001 PHE A 168 TYR 0.021 0.001 TYR G 571 ARG 0.002 0.000 ARG D 201 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 1189) hydrogen bonds : angle 4.32145 ( 3549) covalent geometry : bond 0.00245 (16208) covalent geometry : angle 0.49262 (21860) *********************** 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 185 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 2.337 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 120 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7631 (tptm) REVERT: A 168 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6280 (t80) REVERT: A 565 MET cc_start: 0.3802 (ppp) cc_final: 0.3441 (ptp) REVERT: B 123 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: B 166 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6603 (tttm) REVERT: C 146 MET cc_start: 0.5827 (tmm) cc_final: 0.4778 (tpt) REVERT: D 127 TYR cc_start: 0.7949 (t80) cc_final: 0.7589 (t80) REVERT: D 197 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5663 (pp) REVERT: E 110 MET cc_start: 0.1810 (mmp) cc_final: 0.1601 (mmp) REVERT: F 73 MET cc_start: 0.0512 (OUTLIER) cc_final: -0.1743 (ttt) REVERT: F 84 GLU cc_start: 0.6582 (tt0) cc_final: 0.5602 (mp0) REVERT: F 146 MET cc_start: 0.4195 (tpp) cc_final: 0.3828 (tpp) REVERT: G 120 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7568 (tptm) outliers start: 46 outliers final: 23 residues processed: 167 average time/residue: 2.1620 time to fit residues: 412.4860 Evaluate side-chains 160 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 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 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 135 VAL Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 166 LYS 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 150 CYS Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 171 ILE 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 135 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 150 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 79 ASN D 204 GLN G 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 = 0.4829 r_free = 0.4829 target = 0.255248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.151329 restraints weight = 54781.455| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.63 r_work: 0.3387 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16208 Z= 0.158 Angle : 0.497 6.971 21860 Z= 0.275 Chirality : 0.034 0.128 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.843 28.906 2174 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.22 % Allowed : 24.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 1928 helix: 1.97 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.011 0.001 HIS A 328 PHE 0.014 0.001 PHE A 168 TYR 0.020 0.001 TYR D 571 ARG 0.002 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 1189) hydrogen bonds : angle 4.26541 ( 3549) covalent geometry : bond 0.00350 (16208) covalent geometry : angle 0.49673 (21860) *********************** 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 192 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 2.636 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 120 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7632 (tptm) REVERT: A 123 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: A 133 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7886 (t) REVERT: A 158 ARG cc_start: 0.6674 (tpm-80) cc_final: 0.6422 (mmm160) REVERT: A 168 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6324 (t80) REVERT: A 565 MET cc_start: 0.4000 (ppp) cc_final: 0.3675 (ptp) REVERT: B 123 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: B 166 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6531 (tttm) REVERT: B 211 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6111 (mpp) REVERT: C 73 MET cc_start: 0.0568 (mmp) cc_final: -0.2694 (tpt) REVERT: C 146 MET cc_start: 0.5759 (tmm) cc_final: 0.4700 (tpt) REVERT: D 127 TYR cc_start: 0.7913 (t80) cc_final: 0.7576 (t80) REVERT: D 197 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5693 (pp) REVERT: D 327 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7441 (pptt) REVERT: F 73 MET cc_start: 0.0592 (OUTLIER) cc_final: -0.1727 (ttt) REVERT: F 84 GLU cc_start: 0.6639 (tt0) cc_final: 0.5677 (mp0) REVERT: F 146 MET cc_start: 0.4228 (tpp) cc_final: 0.3867 (tpp) REVERT: G 120 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7591 (tptm) REVERT: H 110 MET cc_start: 0.1487 (mtm) cc_final: 0.0391 (ptm) outliers start: 54 outliers final: 27 residues processed: 172 average time/residue: 2.1954 time to fit residues: 428.8470 Evaluate side-chains 174 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 168 PHE 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 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 B residue 320 VAL 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 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 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 134 ILE Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 171 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 G 204 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 = 0.254293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147593 restraints weight = 54866.821| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.78 r_work: 0.3329 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1934 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= 0.204 Angle : 0.512 6.037 21860 Z= 0.284 Chirality : 0.035 0.129 2396 Planarity : 0.003 0.039 2760 Dihedral : 3.834 17.737 2172 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.46 % Allowed : 24.58 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 1928 helix: 1.88 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.14 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 PHE 0.015 0.001 PHE A 168 TYR 0.019 0.002 TYR D 571 ARG 0.002 0.000 ARG G 581 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 1189) hydrogen bonds : angle 4.30406 ( 3549) covalent geometry : bond 0.00459 (16208) covalent geometry : angle 0.51229 (21860) *********************** 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 197 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 2.812 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: A 120 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7648 (tptm) REVERT: A 123 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 133 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7862 (t) REVERT: A 158 ARG cc_start: 0.6672 (tpm-80) cc_final: 0.6420 (mmm160) REVERT: A 168 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6310 (t80) REVERT: A 565 MET cc_start: 0.3728 (ppp) cc_final: 0.3452 (ptp) REVERT: B 123 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: B 166 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6557 (tttm) REVERT: C 146 MET cc_start: 0.5702 (tmm) cc_final: 0.4654 (tpt) REVERT: D 127 TYR cc_start: 0.7919 (t80) cc_final: 0.7579 (t80) REVERT: D 197 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5684 (pp) REVERT: D 289 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8059 (m-40) REVERT: D 327 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7428 (pptt) REVERT: F 73 MET cc_start: 0.0544 (OUTLIER) cc_final: -0.1703 (ttt) REVERT: F 77 MET cc_start: 0.0021 (OUTLIER) cc_final: -0.0544 (pp-130) REVERT: F 84 GLU cc_start: 0.6649 (tt0) cc_final: 0.5708 (mp0) REVERT: F 146 MET cc_start: 0.4184 (tpp) cc_final: 0.3983 (tpp) REVERT: G 120 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7624 (tptm) REVERT: G 133 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7874 (t) REVERT: G 330 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5524 (pm20) outliers start: 58 outliers final: 32 residues processed: 176 average time/residue: 2.9155 time to fit residues: 595.1361 Evaluate side-chains 181 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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 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 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 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 320 VAL 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 327 LYS 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 262 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 153 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 G 204 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 = 0.4823 r_free = 0.4823 target = 0.254839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149230 restraints weight = 54907.618| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.18 r_work: 0.3353 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16208 Z= 0.172 Angle : 0.504 6.075 21860 Z= 0.278 Chirality : 0.034 0.129 2396 Planarity : 0.004 0.070 2760 Dihedral : 3.812 17.328 2172 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.22 % Allowed : 25.06 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.19), residues: 1928 helix: 1.98 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.24 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.010 0.001 HIS A 328 PHE 0.021 0.001 PHE E 90 TYR 0.019 0.002 TYR D 571 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 1189) hydrogen bonds : angle 4.22894 ( 3549) covalent geometry : bond 0.00383 (16208) covalent geometry : angle 0.50380 (21860) *********************** 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 197 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 2.354 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 120 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7625 (tptm) REVERT: A 123 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: A 133 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7826 (t) REVERT: A 158 ARG cc_start: 0.6673 (tpm-80) cc_final: 0.6413 (mmm160) REVERT: A 168 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.6318 (t80) REVERT: A 565 MET cc_start: 0.3787 (ppp) cc_final: 0.3527 (ptp) REVERT: B 123 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: B 133 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7845 (t) REVERT: B 166 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6430 (tttm) REVERT: B 197 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5663 (pp) REVERT: B 211 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6433 (mpp) REVERT: C 146 MET cc_start: 0.5784 (tmm) cc_final: 0.4738 (tpt) REVERT: D 127 TYR cc_start: 0.7908 (t80) cc_final: 0.7566 (t80) REVERT: D 157 TRP cc_start: 0.5530 (m100) cc_final: 0.5130 (m100) REVERT: D 197 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5745 (pp) REVERT: D 327 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7438 (pptt) REVERT: F 73 MET cc_start: 0.0385 (OUTLIER) cc_final: -0.1867 (ttt) REVERT: F 77 MET cc_start: 0.0034 (OUTLIER) cc_final: -0.0357 (pp-130) REVERT: F 84 GLU cc_start: 0.6672 (tt0) cc_final: 0.5716 (mp0) REVERT: F 146 MET cc_start: 0.4161 (tpp) cc_final: 0.3924 (tpp) REVERT: G 120 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7606 (tptm) REVERT: G 133 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7842 (t) outliers start: 54 outliers final: 31 residues processed: 176 average time/residue: 2.1098 time to fit residues: 425.9991 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 : 2.253 ------------------------------------------------------------------------------- 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 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 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 123 GLU Chi-restraints excluded: chain B residue 133 THR 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 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 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 289 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 LYS 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 262 ASP Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 chunk 169 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.256687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152410 restraints weight = 54994.981| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.49 r_work: 0.3433 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.116 Angle : 0.479 6.519 21860 Z= 0.263 Chirality : 0.033 0.128 2396 Planarity : 0.003 0.060 2760 Dihedral : 3.672 16.423 2172 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.74 % Allowed : 25.66 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.19), residues: 1928 helix: 2.19 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.19 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.007 0.001 HIS A 328 PHE 0.023 0.001 PHE E 90 TYR 0.020 0.001 TYR D 571 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 1189) hydrogen bonds : angle 4.06999 ( 3549) covalent geometry : bond 0.00250 (16208) covalent geometry : angle 0.47938 (21860) *********************** 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 190 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 2.420 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: symmetry clash REVERT: A 120 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7589 (tptm) REVERT: A 158 ARG cc_start: 0.6709 (tpm-80) cc_final: 0.6418 (mmm160) REVERT: A 168 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 565 MET cc_start: 0.4157 (ppp) cc_final: 0.3831 (ptp) REVERT: B 123 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: B 133 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7814 (t) REVERT: B 166 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6460 (tttm) REVERT: B 197 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5490 (pp) REVERT: B 211 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6414 (mpp) REVERT: C 73 MET cc_start: 0.0684 (mmp) cc_final: -0.2754 (tpt) REVERT: C 146 MET cc_start: 0.5769 (tmm) cc_final: 0.4728 (tpt) REVERT: D 127 TYR cc_start: 0.7915 (t80) cc_final: 0.7528 (t80) REVERT: D 157 TRP cc_start: 0.5592 (m100) cc_final: 0.5168 (m100) REVERT: D 197 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5674 (pp) REVERT: D 327 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7451 (pptt) REVERT: F 84 GLU cc_start: 0.6633 (tt0) cc_final: 0.5639 (mp0) REVERT: F 146 MET cc_start: 0.4165 (tpp) cc_final: 0.3812 (tpp) REVERT: G 120 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7531 (tptm) REVERT: G 133 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7808 (t) outliers start: 46 outliers final: 27 residues processed: 176 average time/residue: 2.1708 time to fit residues: 436.4580 Evaluate side-chains 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 199 SER 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 133 THR 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 D residue 84 VAL Chi-restraints excluded: chain D residue 89 ARG 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 289 ASN Chi-restraints excluded: chain D residue 327 LYS 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 150 CYS Chi-restraints excluded: chain G residue 171 ILE 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 167 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 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 = 0.256156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153036 restraints weight = 54923.933| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.44 r_work: 0.3389 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16208 Z= 0.155 Angle : 0.496 6.602 21860 Z= 0.272 Chirality : 0.034 0.128 2396 Planarity : 0.003 0.069 2760 Dihedral : 3.709 16.524 2172 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 26.13 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.19), residues: 1928 helix: 2.19 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.009 0.001 HIS A 328 PHE 0.021 0.001 PHE E 90 TYR 0.019 0.001 TYR D 571 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1189) hydrogen bonds : angle 4.11227 ( 3549) covalent geometry : bond 0.00345 (16208) covalent geometry : angle 0.49565 (21860) *********************** 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 189 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 3.223 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: 0.7960 (OUTLIER) cc_final: 0.7656 (tptm) REVERT: A 158 ARG cc_start: 0.6753 (tpm-80) cc_final: 0.6464 (mmm160) REVERT: A 168 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6393 (t80) REVERT: A 565 MET cc_start: 0.4179 (ppp) cc_final: 0.3842 (ptp) REVERT: B 123 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 133 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7870 (t) REVERT: B 166 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6554 (tttm) REVERT: B 197 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5559 (pp) REVERT: B 211 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6361 (mpp) REVERT: C 146 MET cc_start: 0.5779 (tmm) cc_final: 0.4731 (tpt) REVERT: D 127 TYR cc_start: 0.7961 (t80) cc_final: 0.7568 (t80) REVERT: D 157 TRP cc_start: 0.5562 (m100) cc_final: 0.5157 (m100) REVERT: D 197 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5679 (pp) REVERT: D 289 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8068 (m-40) REVERT: D 327 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7480 (pptt) REVERT: F 73 MET cc_start: 0.0337 (OUTLIER) cc_final: -0.2143 (ttt) REVERT: F 84 GLU cc_start: 0.6715 (tt0) cc_final: 0.5704 (mp0) REVERT: F 146 MET cc_start: 0.4270 (tpp) cc_final: 0.3910 (tpp) REVERT: G 120 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7604 (tptm) REVERT: G 133 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7890 (t) outliers start: 43 outliers final: 26 residues processed: 175 average time/residue: 3.1222 time to fit residues: 654.4035 Evaluate side-chains 179 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 4.036 ------------------------------------------------------------------------------- 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 150 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 199 SER 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 133 THR 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 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 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 289 ASN Chi-restraints excluded: chain D residue 327 LYS 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 150 CYS Chi-restraints excluded: chain G residue 171 ILE 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 126 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 184 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 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 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN D 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.255336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149951 restraints weight = 54910.370| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.48 r_work: 0.3417 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16208 Z= 0.140 Angle : 0.495 7.814 21860 Z= 0.271 Chirality : 0.033 0.128 2396 Planarity : 0.003 0.062 2760 Dihedral : 3.695 16.251 2172 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.68 % Allowed : 26.07 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.19), residues: 1928 helix: 2.22 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.18 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.008 0.001 HIS A 328 PHE 0.021 0.001 PHE E 90 TYR 0.019 0.001 TYR D 571 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 1189) hydrogen bonds : angle 4.07440 ( 3549) covalent geometry : bond 0.00308 (16208) covalent geometry : angle 0.49458 (21860) ********************** 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 184 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 2.298 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: 0.7925 (OUTLIER) cc_final: 0.7617 (tptm) REVERT: A 133 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7778 (t) REVERT: A 158 ARG cc_start: 0.6720 (tpm-80) cc_final: 0.6424 (mmm160) REVERT: A 168 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6356 (t80) REVERT: A 565 MET cc_start: 0.4203 (ppp) cc_final: 0.3599 (ptp) REVERT: A 566 ASP cc_start: 0.3366 (m-30) cc_final: 0.2908 (p0) REVERT: B 123 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: B 133 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7834 (t) REVERT: B 166 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6457 (tttm) REVERT: B 197 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5731 (pp) REVERT: B 211 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6354 (mpp) REVERT: C 73 MET cc_start: 0.0696 (mmp) cc_final: -0.2785 (tpt) REVERT: C 146 MET cc_start: 0.5763 (tmm) cc_final: 0.4732 (tpt) REVERT: D 127 TYR cc_start: 0.7929 (t80) cc_final: 0.7539 (t80) REVERT: D 157 TRP cc_start: 0.5518 (m100) cc_final: 0.5112 (m100) REVERT: D 197 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5716 (pp) REVERT: D 327 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7432 (pptt) REVERT: E 77 MET cc_start: 0.0420 (OUTLIER) cc_final: -0.0739 (mmt) REVERT: F 84 GLU cc_start: 0.6694 (tt0) cc_final: 0.5687 (mp0) REVERT: F 146 MET cc_start: 0.4236 (tpp) cc_final: 0.3893 (tpp) REVERT: G 120 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7574 (tptm) REVERT: G 133 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7792 (t) REVERT: G 565 MET cc_start: 0.3868 (ppp) cc_final: 0.3497 (ptp) REVERT: H 52 MET cc_start: -0.2020 (OUTLIER) cc_final: -0.2991 (ttp) REVERT: H 110 MET cc_start: 0.1740 (mtm) cc_final: 0.0596 (ptm) outliers start: 45 outliers final: 24 residues processed: 169 average time/residue: 2.2832 time to fit residues: 438.6368 Evaluate side-chains 176 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 2.683 ------------------------------------------------------------------------------- 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 168 PHE Chi-restraints excluded: chain A residue 199 SER 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 133 THR 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 D residue 84 VAL Chi-restraints excluded: chain D residue 89 ARG 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 289 ASN Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain E residue 77 MET 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 150 CYS Chi-restraints excluded: chain G residue 171 ILE 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 123 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 G 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.255420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148782 restraints weight = 55006.366| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.82 r_work: 0.3470 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16208 Z= 0.143 Angle : 0.500 7.373 21860 Z= 0.273 Chirality : 0.033 0.128 2396 Planarity : 0.003 0.062 2760 Dihedral : 3.685 16.249 2172 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 26.37 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.19), residues: 1928 helix: 2.24 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.008 0.001 HIS A 328 PHE 0.020 0.001 PHE E 90 TYR 0.019 0.001 TYR D 571 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1189) hydrogen bonds : angle 4.07116 ( 3549) covalent geometry : bond 0.00315 (16208) covalent geometry : angle 0.50021 (21860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34263.34 seconds wall clock time: 590 minutes 14.16 seconds (35414.16 seconds total)