Starting phenix.real_space_refine on Wed Sep 25 09:16:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/09_2024/8ew2_28640.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/09_2024/8ew2_28640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/09_2024/8ew2_28640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/09_2024/8ew2_28640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/09_2024/8ew2_28640.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/09_2024/8ew2_28640.cif" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6516 2.51 5 N 1832 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10340 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "A" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Time building chain proxies: 7.03, per 1000 atoms: 0.68 Number of scatterers: 10340 At special positions: 0 Unit cell: (79.54, 97.58, 104.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1948 8.00 N 1832 7.00 C 6516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 54.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.968A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.536A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.790A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.585A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.984A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.540A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 312 removed outlier: 6.840A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.552A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.514A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.756A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.968A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.525A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 6.314A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.586A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP B 143 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.805A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP A 143 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.959A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE C 269 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.310A pdb=" N GLY D 28 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE D 77 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 30 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE D 269 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 571 hydrogen bonds defined for protein. 1656 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: 3.38 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3441 1.34 - 1.46: 1498 1.46 - 1.57: 5536 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10532 Sorted by residual: bond pdb=" CB PRO D 71 " pdb=" CG PRO D 71 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.331 1.348 -0.017 7.90e-03 1.60e+04 4.55e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.335 1.350 -0.015 9.40e-03 1.13e+04 2.40e+00 bond pdb=" CG1 ILE D 77 " pdb=" CD1 ILE D 77 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.00e+00 bond pdb=" CB GLN C 95 " pdb=" CG GLN C 95 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 ... (remaining 10527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 14040 2.12 - 4.25: 199 4.25 - 6.37: 25 6.37 - 8.50: 3 8.50 - 10.62: 1 Bond angle restraints: 14268 Sorted by residual: angle pdb=" CA PRO D 71 " pdb=" N PRO D 71 " pdb=" CD PRO D 71 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" N VAL B 23 " pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 106.21 110.54 -4.33 1.07e+00 8.73e-01 1.63e+01 angle pdb=" C THR A 51 " pdb=" N GLU A 52 " pdb=" CA GLU A 52 " ideal model delta sigma weight residual 120.82 125.63 -4.81 1.50e+00 4.44e-01 1.03e+01 angle pdb=" N GLU A 49 " pdb=" CA GLU A 49 " pdb=" C GLU A 49 " ideal model delta sigma weight residual 107.73 111.89 -4.16 1.34e+00 5.57e-01 9.63e+00 angle pdb=" N THR A 51 " pdb=" CA THR A 51 " pdb=" C THR A 51 " ideal model delta sigma weight residual 110.35 114.64 -4.29 1.40e+00 5.10e-01 9.39e+00 ... (remaining 14263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5508 17.98 - 35.97: 694 35.97 - 53.95: 167 53.95 - 71.94: 39 71.94 - 89.92: 12 Dihedral angle restraints: 6420 sinusoidal: 2540 harmonic: 3880 Sorted by residual: dihedral pdb=" CA ALA A 304 " pdb=" C ALA A 304 " pdb=" N LEU A 305 " pdb=" CA LEU A 305 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " pdb=" CD GLU B 132 " pdb=" OE1 GLU B 132 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA ASP C 88 " pdb=" CB ASP C 88 " pdb=" CG ASP C 88 " pdb=" OD1 ASP C 88 " ideal model delta sinusoidal sigma weight residual -30.00 -86.17 56.17 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 936 0.026 - 0.051: 393 0.051 - 0.077: 158 0.077 - 0.102: 99 0.102 - 0.128: 42 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CA ILE B 190 " pdb=" N ILE B 190 " pdb=" C ILE B 190 " pdb=" CB ILE B 190 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA TYR C 84 " pdb=" N TYR C 84 " pdb=" C TYR C 84 " pdb=" CB TYR C 84 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1625 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 70 " 0.044 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 71 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 71 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 71 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A 188 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 8 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 9 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.027 5.00e-02 4.00e+02 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 662 2.73 - 3.27: 10885 3.27 - 3.82: 19395 3.82 - 4.36: 23068 4.36 - 4.90: 38736 Nonbonded interactions: 92746 Sorted by model distance: nonbonded pdb=" OE1 GLU A 121 " pdb=" OG SER A 159 " model vdw 2.188 3.040 nonbonded pdb=" NZ LYS B 146 " pdb=" OE1 GLU B 187 " model vdw 2.216 3.120 nonbonded pdb=" OE1 GLU A 81 " pdb=" NE2 GLN A 85 " model vdw 2.220 3.120 nonbonded pdb=" NZ LYS C 207 " pdb=" O SER D 217 " model vdw 2.220 3.120 nonbonded pdb=" O GLN B 60 " pdb=" OG1 THR B 64 " model vdw 2.230 3.040 ... (remaining 92741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.004 0.108 10532 Z= 0.241 Angle : 0.626 10.619 14268 Z= 0.353 Chirality : 0.040 0.128 1628 Planarity : 0.005 0.064 1848 Dihedral : 17.049 89.921 3932 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.46 % Allowed : 21.72 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1340 helix: 1.69 (0.19), residues: 696 sheet: -1.46 (0.38), residues: 192 loop : -0.61 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 147 HIS 0.003 0.001 HIS B 80 PHE 0.010 0.001 PHE A 93 TYR 0.026 0.002 TYR B 58 ARG 0.006 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.210 Fit side-chains REVERT: C 84 TYR cc_start: 0.6279 (m-10) cc_final: 0.6030 (m-10) outliers start: 5 outliers final: 4 residues processed: 118 average time/residue: 0.2303 time to fit residues: 38.9124 Evaluate side-chains 109 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10532 Z= 0.285 Angle : 0.556 7.247 14268 Z= 0.286 Chirality : 0.041 0.133 1628 Planarity : 0.005 0.054 1848 Dihedral : 4.839 59.606 1460 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.28 % Allowed : 19.07 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1340 helix: 1.76 (0.19), residues: 696 sheet: -1.32 (0.35), residues: 216 loop : -0.81 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 147 HIS 0.003 0.001 HIS C 80 PHE 0.010 0.002 PHE A 93 TYR 0.020 0.002 TYR D 213 ARG 0.003 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 1.208 Fit side-chains REVERT: C 303 ARG cc_start: 0.7944 (ptt180) cc_final: 0.7225 (ttt180) REVERT: D 36 THR cc_start: 0.7271 (m) cc_final: 0.6866 (t) REVERT: D 173 TYR cc_start: 0.9257 (OUTLIER) cc_final: 0.8972 (t80) REVERT: D 295 TRP cc_start: 0.9058 (OUTLIER) cc_final: 0.7500 (m-90) outliers start: 36 outliers final: 21 residues processed: 141 average time/residue: 0.2556 time to fit residues: 49.6070 Evaluate side-chains 131 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.0170 chunk 37 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 166 ASN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10532 Z= 0.186 Angle : 0.490 6.474 14268 Z= 0.252 Chirality : 0.039 0.128 1628 Planarity : 0.004 0.047 1848 Dihedral : 4.465 56.768 1457 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.74 % Allowed : 19.07 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1340 helix: 2.04 (0.19), residues: 696 sheet: -1.40 (0.34), residues: 216 loop : -0.80 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.003 0.000 HIS C 80 PHE 0.010 0.001 PHE D 144 TYR 0.015 0.001 TYR A 301 ARG 0.003 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 1.297 Fit side-chains REVERT: B 173 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.9051 (t80) REVERT: B 295 TRP cc_start: 0.8964 (OUTLIER) cc_final: 0.8363 (m-90) REVERT: A 106 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8787 (tt) REVERT: C 303 ARG cc_start: 0.7917 (ptt180) cc_final: 0.7221 (ttt180) REVERT: D 173 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8900 (t80) outliers start: 41 outliers final: 23 residues processed: 157 average time/residue: 0.2574 time to fit residues: 55.0128 Evaluate side-chains 145 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10532 Z= 0.210 Angle : 0.500 6.319 14268 Z= 0.255 Chirality : 0.039 0.140 1628 Planarity : 0.004 0.042 1848 Dihedral : 4.277 57.061 1456 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.56 % Allowed : 18.70 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1340 helix: 2.14 (0.19), residues: 696 sheet: -1.42 (0.34), residues: 216 loop : -0.81 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 147 HIS 0.004 0.000 HIS C 80 PHE 0.011 0.001 PHE C 144 TYR 0.016 0.001 TYR D 213 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 129 time to evaluate : 1.223 Fit side-chains REVERT: B 173 TYR cc_start: 0.9334 (OUTLIER) cc_final: 0.9093 (t80) REVERT: B 295 TRP cc_start: 0.9014 (OUTLIER) cc_final: 0.8550 (m-90) REVERT: A 84 TYR cc_start: 0.7606 (m-80) cc_final: 0.7389 (m-10) REVERT: A 106 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8751 (tt) REVERT: C 303 ARG cc_start: 0.7948 (ptt180) cc_final: 0.7322 (ttt180) REVERT: D 173 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8916 (t80) outliers start: 50 outliers final: 33 residues processed: 161 average time/residue: 0.2345 time to fit residues: 51.9095 Evaluate side-chains 154 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN A 11 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10532 Z= 0.269 Angle : 0.529 6.291 14268 Z= 0.269 Chirality : 0.041 0.144 1628 Planarity : 0.004 0.042 1848 Dihedral : 4.310 56.804 1456 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.84 % Allowed : 18.07 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1340 helix: 2.04 (0.19), residues: 696 sheet: -1.44 (0.34), residues: 216 loop : -0.83 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 147 HIS 0.003 0.001 HIS C 80 PHE 0.010 0.001 PHE C 144 TYR 0.022 0.002 TYR D 213 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 127 time to evaluate : 0.914 Fit side-chains REVERT: B 173 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.9190 (t80) REVERT: B 295 TRP cc_start: 0.9070 (OUTLIER) cc_final: 0.8788 (m-90) REVERT: A 106 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8771 (tt) REVERT: A 189 GLU cc_start: 0.8167 (tp30) cc_final: 0.7662 (tt0) REVERT: C 303 ARG cc_start: 0.7991 (ptt180) cc_final: 0.7354 (ttt180) REVERT: D 173 TYR cc_start: 0.9278 (OUTLIER) cc_final: 0.9034 (t80) outliers start: 53 outliers final: 39 residues processed: 158 average time/residue: 0.2427 time to fit residues: 52.8002 Evaluate side-chains 159 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 31 optimal weight: 9.9990 chunk 127 optimal weight: 0.0980 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN A 231 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10532 Z= 0.169 Angle : 0.488 6.726 14268 Z= 0.247 Chirality : 0.039 0.133 1628 Planarity : 0.004 0.041 1848 Dihedral : 4.110 54.231 1456 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 20.07 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1340 helix: 2.23 (0.19), residues: 696 sheet: -1.81 (0.36), residues: 176 loop : -0.84 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 295 HIS 0.006 0.000 HIS C 80 PHE 0.009 0.001 PHE C 144 TYR 0.012 0.001 TYR A 301 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.282 Fit side-chains REVERT: B 173 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.9002 (t80) REVERT: B 295 TRP cc_start: 0.9013 (OUTLIER) cc_final: 0.8546 (m-90) REVERT: A 106 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8766 (tt) REVERT: C 84 TYR cc_start: 0.6267 (m-10) cc_final: 0.5982 (m-10) REVERT: C 303 ARG cc_start: 0.7971 (ptt180) cc_final: 0.7353 (ttt180) REVERT: C 332 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8357 (mt) REVERT: D 173 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8847 (t80) outliers start: 42 outliers final: 27 residues processed: 161 average time/residue: 0.2548 time to fit residues: 56.9975 Evaluate side-chains 149 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 127 optimal weight: 0.0670 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10532 Z= 0.248 Angle : 0.531 6.149 14268 Z= 0.269 Chirality : 0.040 0.136 1628 Planarity : 0.004 0.040 1848 Dihedral : 4.163 56.240 1456 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.01 % Allowed : 20.44 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1340 helix: 2.18 (0.19), residues: 696 sheet: -1.47 (0.33), residues: 216 loop : -0.79 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 147 HIS 0.004 0.001 HIS C 80 PHE 0.011 0.001 PHE C 144 TYR 0.021 0.002 TYR A 213 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.190 Fit side-chains REVERT: B 173 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.9179 (t80) REVERT: B 295 TRP cc_start: 0.9065 (OUTLIER) cc_final: 0.8824 (m-90) REVERT: A 106 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8753 (tt) REVERT: A 189 GLU cc_start: 0.8239 (tp30) cc_final: 0.7868 (tp30) REVERT: A 295 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.7323 (m-90) REVERT: A 332 LEU cc_start: 0.8612 (tt) cc_final: 0.8091 (mt) REVERT: C 84 TYR cc_start: 0.6543 (m-10) cc_final: 0.6320 (m-10) REVERT: C 303 ARG cc_start: 0.7976 (ptt180) cc_final: 0.7414 (ttt180) REVERT: D 173 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8990 (t80) REVERT: D 295 TRP cc_start: 0.9014 (OUTLIER) cc_final: 0.7740 (m-90) outliers start: 44 outliers final: 31 residues processed: 148 average time/residue: 0.2474 time to fit residues: 50.8872 Evaluate side-chains 152 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10532 Z= 0.197 Angle : 0.505 6.525 14268 Z= 0.256 Chirality : 0.039 0.133 1628 Planarity : 0.004 0.039 1848 Dihedral : 4.092 55.126 1456 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.74 % Allowed : 20.53 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1340 helix: 2.22 (0.19), residues: 696 sheet: -1.81 (0.36), residues: 176 loop : -0.85 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 147 HIS 0.005 0.000 HIS C 80 PHE 0.010 0.001 PHE C 144 TYR 0.014 0.001 TYR B 213 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 122 time to evaluate : 1.212 Fit side-chains REVERT: B 173 TYR cc_start: 0.9365 (OUTLIER) cc_final: 0.9093 (t80) REVERT: B 295 TRP cc_start: 0.9047 (OUTLIER) cc_final: 0.8809 (m-90) REVERT: A 83 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8441 (tp) REVERT: A 106 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8783 (tt) REVERT: A 189 GLU cc_start: 0.8219 (tp30) cc_final: 0.7880 (tp30) REVERT: A 332 LEU cc_start: 0.8580 (tt) cc_final: 0.8091 (mt) REVERT: C 180 ASN cc_start: 0.9088 (m-40) cc_final: 0.8704 (m-40) REVERT: C 303 ARG cc_start: 0.7951 (ptt180) cc_final: 0.7447 (ttt180) REVERT: D 173 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8894 (t80) outliers start: 41 outliers final: 31 residues processed: 148 average time/residue: 0.2286 time to fit residues: 47.9491 Evaluate side-chains 153 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10532 Z= 0.226 Angle : 0.530 6.743 14268 Z= 0.268 Chirality : 0.040 0.299 1628 Planarity : 0.004 0.039 1848 Dihedral : 4.100 55.756 1456 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.01 % Allowed : 20.71 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1340 helix: 2.20 (0.19), residues: 696 sheet: -1.47 (0.33), residues: 216 loop : -0.81 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 147 HIS 0.007 0.001 HIS C 80 PHE 0.010 0.001 PHE C 144 TYR 0.018 0.001 TYR B 213 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.246 Fit side-chains REVERT: B 173 TYR cc_start: 0.9393 (OUTLIER) cc_final: 0.9174 (t80) REVERT: B 295 TRP cc_start: 0.9062 (OUTLIER) cc_final: 0.8835 (m-90) REVERT: A 106 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (tt) REVERT: A 189 GLU cc_start: 0.8227 (tp30) cc_final: 0.7996 (tp30) REVERT: A 295 TRP cc_start: 0.8983 (OUTLIER) cc_final: 0.7447 (m-90) REVERT: A 332 LEU cc_start: 0.8569 (tt) cc_final: 0.8077 (mt) REVERT: C 84 TYR cc_start: 0.6405 (m-10) cc_final: 0.6015 (m-10) REVERT: C 303 ARG cc_start: 0.7951 (ptt180) cc_final: 0.7458 (ttt180) REVERT: D 173 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8967 (t80) REVERT: D 295 TRP cc_start: 0.8999 (OUTLIER) cc_final: 0.7891 (m-90) outliers start: 44 outliers final: 35 residues processed: 149 average time/residue: 0.2453 time to fit residues: 51.5105 Evaluate side-chains 157 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 329 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 111 optimal weight: 0.0030 chunk 32 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10532 Z= 0.211 Angle : 0.527 6.296 14268 Z= 0.266 Chirality : 0.040 0.289 1628 Planarity : 0.004 0.038 1848 Dihedral : 4.085 55.642 1456 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.92 % Allowed : 20.89 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1340 helix: 2.24 (0.19), residues: 696 sheet: -1.79 (0.36), residues: 176 loop : -0.86 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 295 HIS 0.008 0.001 HIS C 80 PHE 0.011 0.001 PHE C 144 TYR 0.017 0.001 TYR C 213 ARG 0.002 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 121 time to evaluate : 1.232 Fit side-chains REVERT: B 173 TYR cc_start: 0.9382 (OUTLIER) cc_final: 0.9164 (t80) REVERT: B 295 TRP cc_start: 0.9059 (OUTLIER) cc_final: 0.8835 (m-90) REVERT: A 106 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8809 (tt) REVERT: A 189 GLU cc_start: 0.8203 (tp30) cc_final: 0.7984 (tp30) REVERT: A 295 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.7316 (m-90) REVERT: A 332 LEU cc_start: 0.8574 (tt) cc_final: 0.7990 (mt) REVERT: C 84 TYR cc_start: 0.6498 (m-10) cc_final: 0.6094 (m-10) REVERT: C 180 ASN cc_start: 0.9083 (m-40) cc_final: 0.8677 (m-40) REVERT: C 303 ARG cc_start: 0.7967 (ptt180) cc_final: 0.7461 (ttt180) REVERT: D 173 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8952 (t80) outliers start: 43 outliers final: 33 residues processed: 149 average time/residue: 0.2336 time to fit residues: 48.7036 Evaluate side-chains 155 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115726 restraints weight = 13981.265| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.87 r_work: 0.3230 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10532 Z= 0.271 Angle : 0.562 10.209 14268 Z= 0.283 Chirality : 0.042 0.291 1628 Planarity : 0.004 0.038 1848 Dihedral : 4.175 56.558 1456 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.01 % Allowed : 20.62 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1340 helix: 2.12 (0.19), residues: 696 sheet: -1.46 (0.34), residues: 216 loop : -0.82 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 147 HIS 0.006 0.001 HIS C 80 PHE 0.010 0.001 PHE C 144 TYR 0.022 0.002 TYR B 213 ARG 0.002 0.000 ARG D 258 =============================================================================== Job complete usr+sys time: 2309.24 seconds wall clock time: 46 minutes 32.38 seconds (2792.38 seconds total)