Starting phenix.real_space_refine on Tue Jun 10 20:14:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwt_35064/06_2025/8hwt_35064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwt_35064/06_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_35064/06_2025/8hwt_35064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwt_35064/06_2025/8hwt_35064.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwt_35064/06_2025/8hwt_35064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwt_35064/06_2025/8hwt_35064.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.21, per 1000 atoms: 0.77 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.27 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: 2.38 Time building geometry restraints manager: 2.28 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.900 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.950 ------------------------------------------------------------------------------- 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 : 6.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (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 TRP 0.007 0.001 TRP D 36 HIS 0.002 0.001 HIS D 207 PHE 0.017 0.001 PHE A 515 TYR 0.015 0.001 TYR D 58 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.15348 ( 304) hydrogen bonds : angle 6.99718 ( 815) SS BOND : bond 0.00425 ( 13) SS BOND : angle 0.92935 ( 26) covalent geometry : bond 0.00284 ( 8272) covalent geometry : angle 0.55863 (11255) *********************** 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 : 0.922 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: 0.7251 (ttpm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.9804 time to fit residues: 163.8308 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 : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.140645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112680 restraints weight = 26294.293| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.08 r_work: 0.3337 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8285 Z= 0.188 Angle : 0.596 7.379 11281 Z= 0.306 Chirality : 0.045 0.169 1254 Planarity : 0.005 0.050 1447 Dihedral : 4.335 24.661 1153 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.20 % Allowed : 9.14 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1049 helix: -2.12 (0.59), residues: 57 sheet: 1.17 (0.24), residues: 460 loop : -0.59 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS D 35 PHE 0.020 0.002 PHE H 67 TYR 0.020 0.002 TYR D 58 ARG 0.006 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 304) hydrogen bonds : angle 5.86078 ( 815) SS BOND : bond 0.00530 ( 13) SS BOND : angle 1.20826 ( 26) covalent geometry : bond 0.00442 ( 8272) covalent geometry : angle 0.59359 (11255) *********************** 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 159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7690 (ttp-110) REVERT: A 472 ILE cc_start: 0.8874 (mm) cc_final: 0.8640 (mm) REVERT: L 3 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7744 (mm-40) REVERT: L 79 GLN cc_start: 0.8528 (mm110) cc_final: 0.8266 (mm110) REVERT: L 123 GLU cc_start: 0.8190 (mp0) cc_final: 0.7881 (mp0) outliers start: 18 outliers final: 15 residues processed: 145 average time/residue: 0.9888 time to fit residues: 154.0226 Evaluate side-chains 155 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 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 78 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.140387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112839 restraints weight = 24421.253| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.91 r_work: 0.3339 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1199 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= 0.175 Angle : 0.582 6.939 11281 Z= 0.298 Chirality : 0.044 0.167 1254 Planarity : 0.005 0.051 1447 Dihedral : 4.345 24.654 1153 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.09 % Allowed : 12.00 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1049 helix: -1.90 (0.66), residues: 51 sheet: 1.18 (0.24), residues: 461 loop : -0.51 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 PHE 0.014 0.001 PHE H 67 TYR 0.018 0.002 TYR D 106 ARG 0.007 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 304) hydrogen bonds : angle 5.65666 ( 815) SS BOND : bond 0.00507 ( 13) SS BOND : angle 1.16996 ( 26) covalent geometry : bond 0.00412 ( 8272) covalent geometry : angle 0.57964 (11255) *********************** 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 162 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9055 (ttt-90) cc_final: 0.8752 (mtp180) REVERT: A 472 ILE cc_start: 0.8886 (mm) cc_final: 0.8653 (mm) REVERT: H 128 LEU cc_start: 0.7808 (mt) cc_final: 0.7536 (mp) REVERT: L 3 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7720 (mm-40) REVERT: L 79 GLN cc_start: 0.8515 (mm110) cc_final: 0.8248 (mm110) REVERT: L 123 GLU cc_start: 0.8193 (mp0) cc_final: 0.7844 (mp0) outliers start: 17 outliers final: 13 residues processed: 148 average time/residue: 1.0226 time to fit residues: 162.4152 Evaluate side-chains 156 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 5 VAL 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 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 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 27 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 L 6 GLN L 166 GLN E 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111657 restraints weight = 28274.584| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 4.26 r_work: 0.3322 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8285 Z= 0.158 Angle : 0.565 7.311 11281 Z= 0.289 Chirality : 0.044 0.165 1254 Planarity : 0.005 0.055 1447 Dihedral : 4.294 24.481 1153 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 13.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1049 helix: -1.90 (0.63), residues: 57 sheet: 1.14 (0.24), residues: 462 loop : -0.40 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 PHE 0.013 0.001 PHE H 67 TYR 0.017 0.001 TYR D 106 ARG 0.007 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 304) hydrogen bonds : angle 5.51986 ( 815) SS BOND : bond 0.00502 ( 13) SS BOND : angle 1.01558 ( 26) covalent geometry : bond 0.00375 ( 8272) covalent geometry : angle 0.56374 (11255) *********************** 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: 25 poor density : 141 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9051 (ttt-90) cc_final: 0.8749 (mtp180) REVERT: A 472 ILE cc_start: 0.8887 (mm) cc_final: 0.8648 (mm) REVERT: H 128 LEU cc_start: 0.7909 (mt) cc_final: 0.7592 (mp) REVERT: L 3 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7761 (mm-40) REVERT: L 18 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8096 (ttm170) REVERT: L 79 GLN cc_start: 0.8519 (mm110) cc_final: 0.8252 (mm110) REVERT: L 123 GLU cc_start: 0.8272 (mp0) cc_final: 0.7883 (mp0) outliers start: 25 outliers final: 17 residues processed: 151 average time/residue: 0.9580 time to fit residues: 155.7199 Evaluate side-chains 167 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 144 CYS 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 27 GLN 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 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 20 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.0050 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN 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 = 0.3899 r_free = 0.3899 target = 0.142714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114855 restraints weight = 24252.950| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.93 r_work: 0.3370 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 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 = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1434 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= 0.096 Angle : 0.534 8.479 11281 Z= 0.268 Chirality : 0.042 0.161 1254 Planarity : 0.004 0.054 1447 Dihedral : 4.021 22.959 1153 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.20 % Allowed : 15.09 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1049 helix: -2.11 (0.58), residues: 64 sheet: 1.25 (0.24), residues: 459 loop : -0.33 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.000 HIS D 35 PHE 0.009 0.001 PHE H 67 TYR 0.016 0.001 TYR D 152 ARG 0.007 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 304) hydrogen bonds : angle 5.21432 ( 815) SS BOND : bond 0.00353 ( 13) SS BOND : angle 0.79649 ( 26) covalent geometry : bond 0.00226 ( 8272) covalent geometry : angle 0.53348 (11255) *********************** 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 164 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.859 Fit side-chains REVERT: A 457 ARG cc_start: 0.9070 (ttt-90) cc_final: 0.8759 (mtp180) REVERT: A 472 ILE cc_start: 0.8864 (mm) cc_final: 0.8627 (mm) REVERT: L 3 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7756 (mm-40) REVERT: L 79 GLN cc_start: 0.8483 (mm110) cc_final: 0.8254 (mm110) REVERT: L 123 GLU cc_start: 0.8195 (mp0) cc_final: 0.7834 (mp0) REVERT: E 23 CYS cc_start: 0.7173 (t) cc_final: 0.6799 (t) REVERT: E 140 PHE cc_start: 0.7959 (p90) cc_final: 0.7638 (p90) outliers start: 18 outliers final: 13 residues processed: 154 average time/residue: 0.9294 time to fit residues: 154.4983 Evaluate side-chains 160 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 144 CYS 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 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 E residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112196 restraints weight = 26041.166| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.02 r_work: 0.3321 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1547 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= 0.199 Angle : 0.592 8.199 11281 Z= 0.303 Chirality : 0.044 0.171 1254 Planarity : 0.005 0.076 1447 Dihedral : 4.269 24.203 1153 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.08 % Allowed : 15.86 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1049 helix: -1.90 (0.63), residues: 57 sheet: 1.19 (0.24), residues: 458 loop : -0.34 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS D 35 PHE 0.016 0.002 PHE L 116 TYR 0.019 0.002 TYR H 33 ARG 0.006 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 304) hydrogen bonds : angle 5.44597 ( 815) SS BOND : bond 0.00557 ( 13) SS BOND : angle 1.15760 ( 26) covalent geometry : bond 0.00469 ( 8272) covalent geometry : angle 0.58991 (11255) *********************** 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 183 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.9057 (ttt-90) cc_final: 0.8749 (mtp180) REVERT: A 472 ILE cc_start: 0.8895 (mm) cc_final: 0.8664 (mm) REVERT: L 3 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7768 (mm-40) REVERT: L 18 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8192 (ttm170) REVERT: L 79 GLN cc_start: 0.8527 (mm110) cc_final: 0.8267 (mm110) REVERT: L 123 GLU cc_start: 0.8255 (mp0) cc_final: 0.7875 (mp0) REVERT: L 169 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8514 (mmtp) REVERT: E 4 MET cc_start: 0.8326 (mmm) cc_final: 0.7835 (mmm) outliers start: 26 outliers final: 17 residues processed: 166 average time/residue: 0.8998 time to fit residues: 161.1682 Evaluate side-chains 171 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 E residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.0370 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 98 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN H 39 GLN L 6 GLN L 89 GLN E 6 GLN E 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112653 restraints weight = 37027.903| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.94 r_work: 0.3308 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8285 Z= 0.108 Angle : 0.546 7.891 11281 Z= 0.275 Chirality : 0.043 0.159 1254 Planarity : 0.005 0.060 1447 Dihedral : 4.054 23.121 1153 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.53 % Allowed : 16.96 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1049 helix: -2.06 (0.60), residues: 62 sheet: 1.26 (0.24), residues: 457 loop : -0.31 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS D 35 PHE 0.009 0.001 PHE H 67 TYR 0.013 0.001 TYR L 96 ARG 0.007 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 304) hydrogen bonds : angle 5.17914 ( 815) SS BOND : bond 0.00380 ( 13) SS BOND : angle 0.85819 ( 26) covalent geometry : bond 0.00257 ( 8272) covalent geometry : angle 0.54546 (11255) *********************** 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 171 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.710 Fit side-chains REVERT: A 457 ARG cc_start: 0.9052 (ttt-90) cc_final: 0.8756 (mtp180) REVERT: A 472 ILE cc_start: 0.8890 (mm) cc_final: 0.8648 (mm) REVERT: L 3 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7785 (mm-40) REVERT: L 18 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8255 (ttm170) REVERT: L 79 GLN cc_start: 0.8585 (mm110) cc_final: 0.8347 (mm110) REVERT: L 123 GLU cc_start: 0.8231 (mp0) cc_final: 0.7846 (mp0) REVERT: L 169 LYS cc_start: 0.8829 (mmtp) cc_final: 0.8557 (mmtp) REVERT: E 23 CYS cc_start: 0.7378 (t) cc_final: 0.6992 (t) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 0.8976 time to fit residues: 154.2400 Evaluate side-chains 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 11 LEU 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 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 E residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 6 GLN L 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111902 restraints weight = 26837.932| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.14 r_work: 0.3323 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1649 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= 0.183 Angle : 0.597 8.773 11281 Z= 0.301 Chirality : 0.044 0.167 1254 Planarity : 0.005 0.063 1447 Dihedral : 4.233 23.787 1153 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.75 % Allowed : 17.62 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1049 helix: -1.87 (0.64), residues: 56 sheet: 1.21 (0.24), residues: 458 loop : -0.33 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 PHE 0.023 0.002 PHE H 67 TYR 0.018 0.002 TYR H 33 ARG 0.011 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 304) hydrogen bonds : angle 5.37201 ( 815) SS BOND : bond 0.00541 ( 13) SS BOND : angle 1.12060 ( 26) covalent geometry : bond 0.00434 ( 8272) covalent geometry : angle 0.59561 (11255) *********************** 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 175 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 472 ILE cc_start: 0.8885 (mm) cc_final: 0.8652 (mm) REVERT: H 128 LEU cc_start: 0.7893 (mt) cc_final: 0.7654 (mp) REVERT: L 3 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7761 (mm-40) REVERT: L 18 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8185 (ttm170) REVERT: L 79 GLN cc_start: 0.8546 (mm110) cc_final: 0.8286 (mm110) REVERT: L 123 GLU cc_start: 0.8249 (mp0) cc_final: 0.7862 (mp0) REVERT: L 169 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8520 (mmtp) outliers start: 23 outliers final: 18 residues processed: 159 average time/residue: 0.9468 time to fit residues: 162.2045 Evaluate side-chains 169 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 74 THR Chi-restraints excluded: chain L residue 132 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 L 6 GLN L 89 GLN E 6 GLN E 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113503 restraints weight = 21033.948| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.64 r_work: 0.3364 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 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 = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8285 Z= 0.139 Angle : 0.579 8.383 11281 Z= 0.290 Chirality : 0.043 0.165 1254 Planarity : 0.005 0.064 1447 Dihedral : 4.182 23.452 1153 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.64 % Allowed : 17.73 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1049 helix: -2.11 (0.60), residues: 62 sheet: 1.24 (0.24), residues: 458 loop : -0.38 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 PHE 0.020 0.001 PHE H 67 TYR 0.016 0.001 TYR L 96 ARG 0.011 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 304) hydrogen bonds : angle 5.28082 ( 815) SS BOND : bond 0.00456 ( 13) SS BOND : angle 1.00795 ( 26) covalent geometry : bond 0.00331 ( 8272) covalent geometry : angle 0.57808 (11255) *********************** 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 164 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 472 ILE cc_start: 0.8877 (mm) cc_final: 0.8638 (mm) REVERT: L 3 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7682 (mm-40) REVERT: L 18 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8137 (ttm170) REVERT: L 79 GLN cc_start: 0.8494 (mm110) cc_final: 0.8234 (mm110) REVERT: L 100 GLN cc_start: 0.8824 (pt0) cc_final: 0.8602 (pt0) REVERT: L 123 GLU cc_start: 0.8216 (mp0) cc_final: 0.7825 (mp0) REVERT: L 169 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8450 (mmtp) REVERT: E 4 MET cc_start: 0.8287 (mmm) cc_final: 0.7914 (mmm) outliers start: 22 outliers final: 19 residues processed: 151 average time/residue: 0.8445 time to fit residues: 138.5554 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 : 0.829 ------------------------------------------------------------------------------- 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 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 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 63 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 8 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 66 optimal weight: 0.0010 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 L 89 GLN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114157 restraints weight = 24121.750| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.89 r_work: 0.3355 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 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 = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8285 Z= 0.130 Angle : 0.575 8.021 11281 Z= 0.287 Chirality : 0.043 0.166 1254 Planarity : 0.005 0.063 1447 Dihedral : 4.117 23.037 1153 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.53 % Allowed : 17.84 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1049 helix: -2.09 (0.60), residues: 62 sheet: 1.25 (0.24), residues: 458 loop : -0.34 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS D 35 PHE 0.021 0.001 PHE A 374 TYR 0.014 0.001 TYR L 96 ARG 0.011 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 304) hydrogen bonds : angle 5.21816 ( 815) SS BOND : bond 0.00435 ( 13) SS BOND : angle 0.94744 ( 26) covalent geometry : bond 0.00310 ( 8272) covalent geometry : angle 0.57376 (11255) ********************** 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 175 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 472 ILE cc_start: 0.8869 (mm) cc_final: 0.8633 (mm) REVERT: L 3 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7703 (mm-40) REVERT: L 18 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8200 (ttm170) REVERT: L 79 GLN cc_start: 0.8497 (mm110) cc_final: 0.8249 (mm110) REVERT: L 100 GLN cc_start: 0.8831 (pt0) cc_final: 0.8597 (pt0) REVERT: L 123 GLU cc_start: 0.8212 (mp0) cc_final: 0.7825 (mp0) REVERT: L 169 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8513 (mmtp) REVERT: E 4 MET cc_start: 0.8310 (mmm) cc_final: 0.7962 (mmm) REVERT: E 23 CYS cc_start: 0.7178 (t) cc_final: 0.6767 (t) outliers start: 21 outliers final: 18 residues processed: 160 average time/residue: 0.9108 time to fit residues: 157.3709 Evaluate side-chains 168 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 D residue 63 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 98 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 25 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 L 89 GLN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113071 restraints weight = 25550.210| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.01 r_work: 0.3338 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8285 Z= 0.162 Angle : 0.602 8.747 11281 Z= 0.299 Chirality : 0.044 0.169 1254 Planarity : 0.005 0.065 1447 Dihedral : 4.237 23.657 1153 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.75 % Allowed : 17.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1049 helix: -2.13 (0.60), residues: 62 sheet: 1.26 (0.24), residues: 458 loop : -0.38 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 35 PHE 0.026 0.002 PHE A 374 TYR 0.016 0.001 TYR H 33 ARG 0.012 0.001 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 304) hydrogen bonds : angle 5.30421 ( 815) SS BOND : bond 0.00507 ( 13) SS BOND : angle 1.06766 ( 26) covalent geometry : bond 0.00385 ( 8272) covalent geometry : angle 0.60078 (11255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6371.18 seconds wall clock time: 109 minutes 17.22 seconds (6557.22 seconds total)