Starting phenix.real_space_refine on Sat Aug 23 12:19:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwt_35064/08_2025/8hwt_35064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwt_35064/08_2025/8hwt_35064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwt_35064/08_2025/8hwt_35064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwt_35064/08_2025/8hwt_35064.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwt_35064/08_2025/8hwt_35064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwt_35064/08_2025/8hwt_35064.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4775 atoms to isotropic. 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 32 5.16 5 C 5099 2.51 5 N 1346 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8077 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 189, 1515 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 189, 1515 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 1 bond proxies already assigned to first conformer: 1548 Chain: "H" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1617 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1662 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Time building chain proxies: 2.16, per 1000 atoms: 0.27 Number of scatterers: 8077 At special positions: 0 Unit cell: (68, 110.5, 123.25, 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 32 16.00 O 1600 8.00 N 1346 7.00 C 5099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 223 " - pdb=" SG CYS E 215 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 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: 0.62 Conformation dependent library (CDL) restraints added in 275.0 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 24 sheets defined 10.6% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.613A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.738A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.370A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.926A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.990A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.843A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 86 through 90 removed outlier: 4.038A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.206A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.937A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.336A pdb=" N VAL H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.220A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 136 removed outlier: 5.220A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.741A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.741A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.139A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.702A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.269A pdb=" N ASP D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU D 45 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.850A pdb=" N CYS D 95 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP D 110 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG D 97 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AC2, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.692A pdb=" N LYS D 216 " --> pdb=" O CYS D 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.549A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.900A pdb=" N LEU E 11 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 115 through 119 Processing sheet with id=AC6, first strand: chain 'E' and resid 145 through 151 332 hydrogen bonds defined for protein. 815 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: 1.12 Time building geometry restraints manager: 0.82 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: 2565 1.34 - 1.46: 2064 1.46 - 1.58: 3605 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8272 Sorted by residual: bond pdb=" N ALA E 113 " pdb=" CA ALA E 113 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.55e-02 4.16e+03 5.02e+00 bond pdb=" CA ALA E 113 " pdb=" CB ALA E 113 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.37e-02 5.33e+03 1.80e+00 bond pdb=" CA PRO E 114 " pdb=" C PRO E 114 " ideal model delta sigma weight residual 1.520 1.538 -0.018 1.42e-02 4.96e+03 1.62e+00 bond pdb=" C PRO E 114 " pdb=" O PRO E 114 " ideal model delta sigma weight residual 1.235 1.219 0.016 1.30e-02 5.92e+03 1.54e+00 bond pdb=" CB ASP L 94 " pdb=" CG ASP L 94 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 ... (remaining 8267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 10995 1.60 - 3.21: 223 3.21 - 4.81: 30 4.81 - 6.42: 5 6.42 - 8.02: 2 Bond angle restraints: 11255 Sorted by residual: angle pdb=" N ALA E 113 " pdb=" CA ALA E 113 " pdb=" C ALA E 113 " ideal model delta sigma weight residual 110.31 115.85 -5.54 1.38e+00 5.25e-01 1.61e+01 angle pdb=" N PRO E 114 " pdb=" CA PRO E 114 " pdb=" C PRO E 114 " ideal model delta sigma weight residual 112.47 119.65 -7.18 2.06e+00 2.36e-01 1.22e+01 angle pdb=" C SER L 63 " pdb=" N GLY L 64 " pdb=" CA GLY L 64 " ideal model delta sigma weight residual 122.18 120.26 1.92 6.90e-01 2.10e+00 7.72e+00 angle pdb=" C ALA E 113 " pdb=" N PRO E 114 " pdb=" CA PRO E 114 " ideal model delta sigma weight residual 119.84 122.79 -2.95 1.25e+00 6.40e-01 5.55e+00 angle pdb=" C SER L 93 " pdb=" N ASP L 94 " pdb=" CA ASP L 94 " ideal model delta sigma weight residual 124.82 128.96 -4.14 1.78e+00 3.16e-01 5.42e+00 ... (remaining 11250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4532 17.28 - 34.56: 323 34.56 - 51.83: 56 51.83 - 69.11: 15 69.11 - 86.39: 11 Dihedral angle restraints: 4937 sinusoidal: 1872 harmonic: 3065 Sorted by residual: dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 127.41 -34.41 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CA ASN L 92 " pdb=" C ASN L 92 " pdb=" N SER L 93 " pdb=" CA SER L 93 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 930 0.044 - 0.088: 235 0.088 - 0.131: 85 0.131 - 0.175: 3 0.175 - 0.219: 1 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CA PRO E 114 " pdb=" N PRO E 114 " pdb=" C PRO E 114 " pdb=" CB PRO E 114 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP L 94 " pdb=" N ASP L 94 " pdb=" C ASP L 94 " pdb=" CB ASP L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CB ILE A 358 " pdb=" CA ILE A 358 " pdb=" CG1 ILE A 358 " pdb=" CG2 ILE A 358 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1251 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " -0.039 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO H 153 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 188 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO H 189 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO L 40 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " 0.030 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1386 2.77 - 3.30: 6980 3.30 - 3.84: 12645 3.84 - 4.37: 14696 4.37 - 4.90: 26695 Nonbonded interactions: 62402 Sorted by model distance: nonbonded pdb=" O VAL D 128 " pdb=" NZ LYS D 216 " model vdw 2.241 3.120 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.259 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP H 98 " pdb=" OH TYR L 96 " model vdw 2.273 3.040 nonbonded pdb=" NZ LYS E 39 " pdb=" O GLU E 81 " model vdw 2.287 3.120 ... (remaining 62397 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 'D' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid \ 55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ d 78 through 82 or resid 84 through 87 or resid 89 through 97 or resid 99 or res \ id 102 or resid 104 or resid 108 or resid 110 through 114 or resid 117 through 2 \ 22)) selection = (chain 'H' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid \ 55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ d 78 through 82 or resid 84 through 87 or resid 89 through 98 or resid 100 or re \ sid 102 or resid 105 or resid 107 through 111 or resid 114 through 219)) } ncs_group { reference = (chain 'E' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 13 or \ resid 15 through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 \ or resid 46 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 \ through 90 or resid 94 or resid 97 through 100 or resid 102 through 104 or resi \ d 107 through 214)) selection = (chain 'L' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 13 or \ resid 15 through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 \ or resid 46 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 \ through 90 or resid 93 or resid 96 through 99 or resid 101 through 103 or resid \ 106 through 213)) } 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=0.45 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 0.047 8285 Z= 0.127 Angle : 0.560 8.022 11281 Z= 0.294 Chirality : 0.044 0.219 1254 Planarity : 0.005 0.060 1447 Dihedral : 12.838 86.391 2950 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.26), residues: 1049 helix: -1.57 (0.70), residues: 50 sheet: 1.23 (0.25), residues: 433 loop : -0.47 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.015 0.001 TYR D 58 PHE 0.017 0.001 PHE A 515 TRP 0.007 0.001 TRP D 36 HIS 0.002 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8272) covalent geometry : angle 0.55863 (11255) SS BOND : bond 0.00425 ( 13) SS BOND : angle 0.92935 ( 26) hydrogen bonds : bond 0.15348 ( 304) hydrogen bonds : angle 6.99718 ( 815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8017 (t) cc_final: 0.7781 (p) REVERT: A 346 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.7011 (ttp-110) REVERT: A 472 ILE cc_start: 0.7927 (mm) cc_final: 0.7675 (mm) REVERT: H 109 GLN cc_start: 0.7322 (mm110) cc_final: 0.7020 (mm110) REVERT: L 3 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7307 (mm-40) REVERT: L 79 GLN cc_start: 0.8091 (mm110) cc_final: 0.7838 (mm110) REVERT: L 123 GLU cc_start: 0.8136 (mp0) cc_final: 0.7875 (mp0) REVERT: D 58 TYR cc_start: 0.7542 (m-10) cc_final: 0.7225 (m-80) REVERT: D 116 LEU cc_start: 0.6601 (tp) cc_final: 0.6342 (tt) REVERT: D 124 LYS cc_start: 0.7462 (tmtt) cc_final: 0.7246 (tmtm) REVERT: D 150 LYS cc_start: 0.7046 (tttm) cc_final: 0.6631 (tttm) REVERT: D 152 TYR cc_start: 0.7507 (p90) cc_final: 0.6866 (p90) REVERT: E 6 GLN cc_start: 0.6522 (mt0) cc_final: 0.6308 (mt0) REVERT: E 23 CYS cc_start: 0.5533 (t) cc_final: 0.4924 (t) REVERT: E 108 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7252 (ttpm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3664 time to fit residues: 61.0729 Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN L 6 GLN L 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112211 restraints weight = 26014.087| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 4.06 r_work: 0.3325 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 8285 Z= 0.205 Angle : 0.605 7.349 11281 Z= 0.311 Chirality : 0.045 0.170 1254 Planarity : 0.005 0.050 1447 Dihedral : 4.374 24.767 1153 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.31 % Allowed : 8.81 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.26), residues: 1049 helix: -2.10 (0.59), residues: 57 sheet: 1.14 (0.24), residues: 461 loop : -0.59 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 61 TYR 0.020 0.002 TYR D 58 PHE 0.020 0.002 PHE H 67 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8272) covalent geometry : angle 0.60278 (11255) SS BOND : bond 0.00540 ( 13) SS BOND : angle 1.23288 ( 26) hydrogen bonds : bond 0.03998 ( 304) hydrogen bonds : angle 5.90657 ( 815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7632 (ttp-110) REVERT: A 472 ILE cc_start: 0.8874 (mm) cc_final: 0.8643 (mm) REVERT: L 3 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7736 (mm-40) REVERT: L 79 GLN cc_start: 0.8553 (mm110) cc_final: 0.8288 (mm110) REVERT: L 123 GLU cc_start: 0.8172 (mp0) cc_final: 0.7867 (mp0) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.3819 time to fit residues: 61.2235 Evaluate side-chains 163 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN E 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112460 restraints weight = 25239.597| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.99 r_work: 0.3329 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8285 Z= 0.188 Angle : 0.594 7.333 11281 Z= 0.303 Chirality : 0.044 0.168 1254 Planarity : 0.005 0.052 1447 Dihedral : 4.409 24.543 1153 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.42 % Allowed : 12.00 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 1049 helix: -1.98 (0.66), residues: 51 sheet: 1.12 (0.24), residues: 464 loop : -0.52 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 61 TYR 0.016 0.002 TYR H 33 PHE 0.015 0.002 PHE H 67 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 8272) covalent geometry : angle 0.59169 (11255) SS BOND : bond 0.00515 ( 13) SS BOND : angle 1.24654 ( 26) hydrogen bonds : bond 0.03721 ( 304) hydrogen bonds : angle 5.70382 ( 815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9054 (ttt-90) cc_final: 0.8754 (mtp180) REVERT: A 472 ILE cc_start: 0.8890 (mm) cc_final: 0.8653 (mm) REVERT: H 128 LEU cc_start: 0.7821 (mt) cc_final: 0.7553 (mp) REVERT: H 179 LEU cc_start: 0.8701 (mt) cc_final: 0.8489 (mp) REVERT: L 3 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7729 (mm-40) REVERT: L 79 GLN cc_start: 0.8552 (mm110) cc_final: 0.8270 (mm110) REVERT: L 123 GLU cc_start: 0.8262 (mp0) cc_final: 0.7915 (mp0) REVERT: D 124 LYS cc_start: 0.8234 (tmtp) cc_final: 0.7992 (tmtm) REVERT: D 148 LEU cc_start: 0.8550 (tt) cc_final: 0.8264 (tm) outliers start: 20 outliers final: 15 residues processed: 155 average time/residue: 0.4012 time to fit residues: 66.7537 Evaluate side-chains 159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 6 GLN L 166 GLN E 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113012 restraints weight = 22960.196| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.79 r_work: 0.3349 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8285 Z= 0.163 Angle : 0.577 8.539 11281 Z= 0.293 Chirality : 0.044 0.166 1254 Planarity : 0.005 0.055 1447 Dihedral : 4.329 24.343 1153 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.53 % Allowed : 13.88 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.26), residues: 1049 helix: -1.96 (0.63), residues: 57 sheet: 1.12 (0.24), residues: 461 loop : -0.44 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 61 TYR 0.015 0.001 TYR H 33 PHE 0.013 0.001 PHE L 116 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8272) covalent geometry : angle 0.57574 (11255) SS BOND : bond 0.00537 ( 13) SS BOND : angle 1.03639 ( 26) hydrogen bonds : bond 0.03440 ( 304) hydrogen bonds : angle 5.54584 ( 815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9037 (ttt-90) cc_final: 0.8730 (mtp180) REVERT: A 472 ILE cc_start: 0.8875 (mm) cc_final: 0.8635 (mm) REVERT: H 128 LEU cc_start: 0.7911 (mt) cc_final: 0.7596 (mp) REVERT: H 179 LEU cc_start: 0.8705 (mt) cc_final: 0.8489 (mp) REVERT: L 3 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7749 (mm-40) REVERT: L 79 GLN cc_start: 0.8468 (mm110) cc_final: 0.8196 (mm110) REVERT: L 123 GLU cc_start: 0.8243 (mp0) cc_final: 0.7883 (mp0) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.3810 time to fit residues: 62.3784 Evaluate side-chains 166 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 79 optimal weight: 0.0070 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN L 6 GLN E 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111144 restraints weight = 35448.486| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.82 r_work: 0.3287 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8285 Z= 0.155 Angle : 0.576 7.832 11281 Z= 0.292 Chirality : 0.044 0.166 1254 Planarity : 0.005 0.056 1447 Dihedral : 4.282 24.308 1153 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.08 % Allowed : 14.32 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 1049 helix: -2.21 (0.57), residues: 63 sheet: 1.15 (0.24), residues: 458 loop : -0.45 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 61 TYR 0.015 0.001 TYR H 33 PHE 0.017 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8272) covalent geometry : angle 0.57469 (11255) SS BOND : bond 0.00494 ( 13) SS BOND : angle 1.02366 ( 26) hydrogen bonds : bond 0.03342 ( 304) hydrogen bonds : angle 5.46760 ( 815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9064 (ttt-90) cc_final: 0.8763 (mtp180) REVERT: A 472 ILE cc_start: 0.8893 (mm) cc_final: 0.8651 (mm) REVERT: H 179 LEU cc_start: 0.8746 (mt) cc_final: 0.8524 (mp) REVERT: L 3 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7814 (mm-40) REVERT: L 18 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8172 (ttm170) REVERT: L 79 GLN cc_start: 0.8583 (mm110) cc_final: 0.8302 (mm110) REVERT: L 123 GLU cc_start: 0.8258 (mp0) cc_final: 0.7900 (mp0) REVERT: D 148 LEU cc_start: 0.8566 (tp) cc_final: 0.8311 (tm) outliers start: 26 outliers final: 21 residues processed: 163 average time/residue: 0.4097 time to fit residues: 71.5605 Evaluate side-chains 171 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.139204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111143 restraints weight = 30648.253| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 4.54 r_work: 0.3297 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8285 Z= 0.196 Angle : 0.597 7.717 11281 Z= 0.305 Chirality : 0.044 0.165 1254 Planarity : 0.005 0.078 1447 Dihedral : 4.393 24.696 1153 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.41 % Allowed : 15.31 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1049 helix: -1.98 (0.62), residues: 57 sheet: 1.08 (0.24), residues: 461 loop : -0.37 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 61 TYR 0.018 0.002 TYR H 33 PHE 0.015 0.002 PHE L 116 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8272) covalent geometry : angle 0.59539 (11255) SS BOND : bond 0.00560 ( 13) SS BOND : angle 1.17425 ( 26) hydrogen bonds : bond 0.03605 ( 304) hydrogen bonds : angle 5.53221 ( 815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9055 (ttt-90) cc_final: 0.8751 (mtp180) REVERT: A 472 ILE cc_start: 0.8890 (mm) cc_final: 0.8655 (mm) REVERT: H 179 LEU cc_start: 0.8735 (mt) cc_final: 0.8508 (mp) REVERT: L 3 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7843 (mm-40) REVERT: L 18 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8218 (ttm170) REVERT: L 79 GLN cc_start: 0.8580 (mm110) cc_final: 0.8294 (mm110) REVERT: L 91 LEU cc_start: 0.7950 (tm) cc_final: 0.7592 (mt) REVERT: L 123 GLU cc_start: 0.8257 (mp0) cc_final: 0.7869 (mp0) REVERT: D 148 LEU cc_start: 0.8527 (tp) cc_final: 0.8240 (tm) REVERT: E 4 MET cc_start: 0.8342 (mmm) cc_final: 0.7890 (mmm) outliers start: 29 outliers final: 20 residues processed: 166 average time/residue: 0.3856 time to fit residues: 69.0039 Evaluate side-chains 174 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112757 restraints weight = 25756.534| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.03 r_work: 0.3329 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8285 Z= 0.163 Angle : 0.586 8.602 11281 Z= 0.297 Chirality : 0.044 0.163 1254 Planarity : 0.005 0.063 1447 Dihedral : 4.334 24.366 1153 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.19 % Allowed : 16.08 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.26), residues: 1049 helix: -2.21 (0.58), residues: 63 sheet: 1.12 (0.24), residues: 459 loop : -0.45 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 61 TYR 0.015 0.001 TYR H 33 PHE 0.012 0.001 PHE L 116 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8272) covalent geometry : angle 0.58448 (11255) SS BOND : bond 0.00489 ( 13) SS BOND : angle 1.08177 ( 26) hydrogen bonds : bond 0.03380 ( 304) hydrogen bonds : angle 5.43643 ( 815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9039 (ttt-90) cc_final: 0.8740 (mtp180) REVERT: A 472 ILE cc_start: 0.8891 (mm) cc_final: 0.8643 (mm) REVERT: H 179 LEU cc_start: 0.8725 (mt) cc_final: 0.8506 (mp) REVERT: L 3 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7769 (mm-40) REVERT: L 18 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8231 (ttm170) REVERT: L 79 GLN cc_start: 0.8521 (mm110) cc_final: 0.8237 (mm110) REVERT: L 123 GLU cc_start: 0.8250 (mp0) cc_final: 0.7872 (mp0) REVERT: L 169 LYS cc_start: 0.8786 (mmtp) cc_final: 0.8510 (mmtp) REVERT: D 148 LEU cc_start: 0.8478 (tp) cc_final: 0.8199 (tm) REVERT: E 87 TYR cc_start: 0.8824 (m-80) cc_final: 0.8490 (m-80) outliers start: 27 outliers final: 22 residues processed: 165 average time/residue: 0.3524 time to fit residues: 62.9214 Evaluate side-chains 170 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN E 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111996 restraints weight = 33869.807| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 4.67 r_work: 0.3294 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8285 Z= 0.175 Angle : 0.601 8.059 11281 Z= 0.303 Chirality : 0.044 0.163 1254 Planarity : 0.005 0.064 1447 Dihedral : 4.358 24.186 1153 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.41 % Allowed : 16.30 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1049 helix: -1.97 (0.63), residues: 57 sheet: 1.15 (0.24), residues: 459 loop : -0.41 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 61 TYR 0.016 0.002 TYR H 33 PHE 0.021 0.002 PHE H 67 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8272) covalent geometry : angle 0.59892 (11255) SS BOND : bond 0.00522 ( 13) SS BOND : angle 1.13222 ( 26) hydrogen bonds : bond 0.03467 ( 304) hydrogen bonds : angle 5.46032 ( 815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9049 (ttt-90) cc_final: 0.8756 (mtp180) REVERT: A 472 ILE cc_start: 0.8896 (mm) cc_final: 0.8651 (mm) REVERT: H 179 LEU cc_start: 0.8756 (mt) cc_final: 0.8524 (mp) REVERT: L 3 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7802 (mm-40) REVERT: L 18 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8258 (ttm170) REVERT: L 79 GLN cc_start: 0.8563 (mm110) cc_final: 0.8279 (mm110) REVERT: L 91 LEU cc_start: 0.7928 (tm) cc_final: 0.7708 (tt) REVERT: L 100 GLN cc_start: 0.8872 (pt0) cc_final: 0.8654 (pt0) REVERT: L 123 GLU cc_start: 0.8261 (mp0) cc_final: 0.7846 (mp0) REVERT: L 169 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8543 (mmtp) REVERT: D 148 LEU cc_start: 0.8514 (tp) cc_final: 0.8235 (tm) REVERT: E 87 TYR cc_start: 0.8849 (m-80) cc_final: 0.8516 (m-80) outliers start: 29 outliers final: 23 residues processed: 165 average time/residue: 0.3440 time to fit residues: 61.4396 Evaluate side-chains 179 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.141144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114361 restraints weight = 24339.647| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.85 r_work: 0.3359 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8285 Z= 0.155 Angle : 0.598 7.864 11281 Z= 0.301 Chirality : 0.044 0.162 1254 Planarity : 0.005 0.065 1447 Dihedral : 4.437 24.630 1153 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.08 % Allowed : 16.85 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.26), residues: 1049 helix: -2.24 (0.58), residues: 63 sheet: 1.23 (0.24), residues: 457 loop : -0.50 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 61 TYR 0.016 0.001 TYR H 94 PHE 0.021 0.002 PHE H 67 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8272) covalent geometry : angle 0.59674 (11255) SS BOND : bond 0.00493 ( 13) SS BOND : angle 1.12635 ( 26) hydrogen bonds : bond 0.03313 ( 304) hydrogen bonds : angle 5.42518 ( 815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9047 (ttt-90) cc_final: 0.8751 (mtp180) REVERT: A 472 ILE cc_start: 0.8880 (mm) cc_final: 0.8634 (mm) REVERT: H 85 LEU cc_start: 0.8441 (mt) cc_final: 0.8241 (mp) REVERT: H 179 LEU cc_start: 0.8740 (mt) cc_final: 0.8496 (mp) REVERT: L 3 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7758 (mm-40) REVERT: L 18 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8234 (ttm170) REVERT: L 79 GLN cc_start: 0.8503 (mm110) cc_final: 0.8230 (mm110) REVERT: L 123 GLU cc_start: 0.8187 (mp0) cc_final: 0.7788 (mp0) REVERT: L 169 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8485 (mmtp) REVERT: D 148 LEU cc_start: 0.8444 (tp) cc_final: 0.8152 (tm) REVERT: E 4 MET cc_start: 0.8312 (mmm) cc_final: 0.7928 (mmm) outliers start: 26 outliers final: 23 residues processed: 160 average time/residue: 0.3340 time to fit residues: 58.0533 Evaluate side-chains 170 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.0000 chunk 70 optimal weight: 0.0010 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 76 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 overall best weight: 0.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 6 GLN L 160 GLN E 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.145945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118203 restraints weight = 37766.456| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 5.14 r_work: 0.3367 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8285 Z= 0.091 Angle : 0.539 8.025 11281 Z= 0.269 Chirality : 0.043 0.159 1254 Planarity : 0.004 0.056 1447 Dihedral : 3.935 23.266 1153 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.87 % Allowed : 17.95 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.26), residues: 1049 helix: -2.14 (0.60), residues: 63 sheet: 1.39 (0.24), residues: 445 loop : -0.32 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 61 TYR 0.011 0.001 TYR L 173 PHE 0.014 0.001 PHE A 374 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8272) covalent geometry : angle 0.53857 (11255) SS BOND : bond 0.00210 ( 13) SS BOND : angle 0.84329 ( 26) hydrogen bonds : bond 0.02419 ( 304) hydrogen bonds : angle 4.92567 ( 815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 472 ILE cc_start: 0.8848 (mm) cc_final: 0.8596 (mm) REVERT: H 128 LEU cc_start: 0.7749 (mt) cc_final: 0.7388 (mp) REVERT: H 179 LEU cc_start: 0.8763 (mt) cc_final: 0.8483 (mp) REVERT: L 3 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7925 (mm-40) REVERT: L 52 SER cc_start: 0.8421 (t) cc_final: 0.8206 (m) REVERT: L 123 GLU cc_start: 0.8192 (mp0) cc_final: 0.7815 (mp0) REVERT: L 169 LYS cc_start: 0.8816 (mmtp) cc_final: 0.8580 (mmtp) REVERT: E 4 MET cc_start: 0.8341 (mmm) cc_final: 0.7922 (mmm) REVERT: E 140 PHE cc_start: 0.7975 (p90) cc_final: 0.7651 (p90) outliers start: 15 outliers final: 9 residues processed: 160 average time/residue: 0.3249 time to fit residues: 56.4836 Evaluate side-chains 160 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 12 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 79 GLN L 89 GLN L 160 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.142295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114527 restraints weight = 29396.164| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.30 r_work: 0.3354 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8285 Z= 0.138 Angle : 0.600 11.230 11281 Z= 0.296 Chirality : 0.044 0.164 1254 Planarity : 0.005 0.059 1447 Dihedral : 4.072 23.145 1153 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.32 % Allowed : 19.38 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.26), residues: 1049 helix: -2.12 (0.60), residues: 63 sheet: 1.38 (0.24), residues: 457 loop : -0.32 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 61 TYR 0.015 0.001 TYR H 94 PHE 0.027 0.002 PHE A 374 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8272) covalent geometry : angle 0.59810 (11255) SS BOND : bond 0.00449 ( 13) SS BOND : angle 1.10358 ( 26) hydrogen bonds : bond 0.03021 ( 304) hydrogen bonds : angle 5.07573 ( 815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2576.80 seconds wall clock time: 44 minutes 32.50 seconds (2672.50 seconds total)