Starting phenix.real_space_refine on Sun Dec 29 16:52:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpu_34944/12_2024/8hpu_34944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpu_34944/12_2024/8hpu_34944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpu_34944/12_2024/8hpu_34944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpu_34944/12_2024/8hpu_34944.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpu_34944/12_2024/8hpu_34944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpu_34944/12_2024/8hpu_34944.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.075 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 3142 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 34 5.16 5 C 5224 2.51 5 N 1390 2.21 5 O 1633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8281 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1555 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Conformer: "B" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} bond proxies already assigned to first conformer: 1584 Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.95, per 1000 atoms: 0.96 Number of scatterers: 8281 At special positions: 0 Unit cell: (117.6, 124.32, 120.12, 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 34 16.00 O 1633 8.00 N 1390 7.00 C 5224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 375 " distance=2.03 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 539 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.04 Simple disulfide: pdb=" SG CYS H 231 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.04 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.04 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 Links applied NAG-ASN " NAG A1201 " - " ASN A 357 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.3 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 23 sheets defined 8.4% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.583A pdb=" N VAL A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.564A pdb=" N TRP A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 385 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.869A pdb=" N LEU A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 404 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.644A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.796A pdb=" N LEU H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 196 through 201 removed outlier: 4.488A pdb=" N THR M 200 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 185 through 190 removed outlier: 3.867A pdb=" N LYS N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 372 Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 468 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 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: 6.194A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.350A pdb=" N PHE H 101 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE H 115 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.212A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.212A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.180A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.954A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 145 through 151 Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.825A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.389A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.732A pdb=" N CYS M 95 " --> pdb=" O TRP M 112 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP M 112 " --> pdb=" O CYS M 95 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG M 97 " --> pdb=" O ASP M 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA M 108 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 160 through 163 removed outlier: 3.586A pdb=" N TYR M 203 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.630A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.618A pdb=" N GLU N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 116 through 120 removed outlier: 5.744A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER N 176 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 155 through 157 removed outlier: 4.155A pdb=" N TRP N 150 " --> pdb=" O GLN N 157 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 879 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: 2.67 Time building geometry restraints manager: 2.40 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: 2642 1.34 - 1.46: 2053 1.46 - 1.58: 3752 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 8487 Sorted by residual: bond pdb=" CA CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.53e-02 4.27e+03 5.06e+00 bond pdb=" C PHE M 102 " pdb=" N PRO M 103 " ideal model delta sigma weight residual 1.334 1.345 -0.012 8.40e-03 1.42e+04 1.99e+00 bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C ALA A 386 " pdb=" N PRO A 387 " ideal model delta sigma weight residual 1.337 1.350 -0.014 1.06e-02 8.90e+03 1.66e+00 bond pdb=" C ASP N 187 " pdb=" N TYR N 188 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.40e-02 5.10e+03 1.49e+00 ... (remaining 8482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 11476 3.11 - 6.23: 70 6.23 - 9.34: 5 9.34 - 12.46: 0 12.46 - 15.57: 2 Bond angle restraints: 11553 Sorted by residual: angle pdb=" C LEU H 139 " pdb=" N ALA H 140 " pdb=" CA ALA H 140 " ideal model delta sigma weight residual 120.94 136.51 -15.57 1.90e+00 2.77e-01 6.72e+01 angle pdb=" CA CYS A 446 " pdb=" CB CYS A 446 " pdb=" SG CYS A 446 " ideal model delta sigma weight residual 114.40 128.26 -13.86 2.30e+00 1.89e-01 3.63e+01 angle pdb=" N CYS A 393 " pdb=" CA CYS A 393 " pdb=" C CYS A 393 " ideal model delta sigma weight residual 107.88 116.19 -8.31 1.41e+00 5.03e-01 3.47e+01 angle pdb=" N CYS A 446 " pdb=" CA CYS A 446 " pdb=" C CYS A 446 " ideal model delta sigma weight residual 107.88 113.55 -5.67 1.41e+00 5.03e-01 1.61e+01 angle pdb=" CA GLY A 445 " pdb=" C GLY A 445 " pdb=" O GLY A 445 " ideal model delta sigma weight residual 122.24 117.97 4.27 1.08e+00 8.57e-01 1.56e+01 ... (remaining 11548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4625 17.65 - 35.31: 366 35.31 - 52.96: 68 52.96 - 70.61: 15 70.61 - 88.26: 13 Dihedral angle restraints: 5087 sinusoidal: 1963 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ASP H 116 " pdb=" C ASP H 116 " pdb=" N PRO H 117 " pdb=" CA PRO H 117 " ideal model delta harmonic sigma weight residual -180.00 -131.45 -48.55 0 5.00e+00 4.00e-02 9.43e+01 dihedral pdb=" CB CYS A 393 " pdb=" SG CYS A 393 " pdb=" SG CYS A 446 " pdb=" CB CYS A 446 " ideal model delta sinusoidal sigma weight residual -86.00 -11.06 -74.94 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS H 155 " pdb=" SG CYS H 155 " pdb=" SG CYS H 211 " pdb=" CB CYS H 211 " ideal model delta sinusoidal sigma weight residual 93.00 154.84 -61.84 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 5084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1001 0.051 - 0.101: 231 0.101 - 0.152: 54 0.152 - 0.203: 3 0.203 - 0.253: 1 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CA CYS A 393 " pdb=" N CYS A 393 " pdb=" C CYS A 393 " pdb=" CB CYS A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LYS M 215 " pdb=" N LYS M 215 " pdb=" C LYS M 215 " pdb=" CB LYS M 215 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA CYS A 446 " pdb=" N CYS A 446 " pdb=" C CYS A 446 " pdb=" CB CYS A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1287 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 163 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO H 164 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 164 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 164 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 116 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO H 117 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 117 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 117 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 131 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO M 132 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO M 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 132 " -0.026 5.00e-02 4.00e+02 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 832 2.75 - 3.29: 7851 3.29 - 3.83: 13703 3.83 - 4.36: 16707 4.36 - 4.90: 28781 Nonbonded interactions: 67874 Sorted by model distance: nonbonded pdb=" NH2 ARG N 61 " pdb=" OE2 GLU N 81 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASP A 456 " pdb=" OH TYR A 465 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 514 " pdb=" OH TYR L 33 " model vdw 2.258 3.040 nonbonded pdb=" CB CYS A 393 " pdb=" CB CYS A 446 " model vdw 2.276 3.072 nonbonded pdb=" NE2 GLN L 148 " pdb=" O GLN L 156 " model vdw 2.286 3.120 ... (remaining 67869 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 8.820 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.450 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 0.044 8487 Z= 0.206 Angle : 0.692 15.572 11553 Z= 0.365 Chirality : 0.046 0.253 1290 Planarity : 0.005 0.057 1488 Dihedral : 13.597 88.265 3049 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.11 % Allowed : 0.21 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.10 % 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: -0.21 (0.26), residues: 1071 helix: -2.94 (0.64), residues: 41 sheet: 0.91 (0.25), residues: 427 loop : -0.72 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 150 HIS 0.010 0.001 HIS A 519 PHE 0.017 0.001 PHE A 391 TYR 0.018 0.002 TYR L 174 ARG 0.003 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6168 (p90) cc_final: 0.5852 (p90) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.4103 time to fit residues: 198.3356 Evaluate side-chains 86 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.2980 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 HIS H 219 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN N 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8487 Z= 0.185 Angle : 0.636 15.000 11553 Z= 0.328 Chirality : 0.045 0.184 1290 Planarity : 0.005 0.062 1488 Dihedral : 5.304 45.412 1189 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.61 % Allowed : 9.11 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.02 (0.26), residues: 1071 helix: -2.92 (0.63), residues: 40 sheet: 1.07 (0.25), residues: 424 loop : -0.59 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 149 HIS 0.008 0.001 HIS A 519 PHE 0.014 0.001 PHE N 141 TYR 0.015 0.001 TYR L 141 ARG 0.008 0.001 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 405 CYS cc_start: 0.4033 (t) cc_final: 0.3792 (t) REVERT: H 160 TYR cc_start: 0.6212 (p90) cc_final: 0.5844 (p90) outliers start: 14 outliers final: 2 residues processed: 107 average time/residue: 1.1854 time to fit residues: 135.6141 Evaluate side-chains 85 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain N residue 138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 214 ASN H 219 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8487 Z= 0.265 Angle : 0.675 16.643 11553 Z= 0.349 Chirality : 0.047 0.200 1290 Planarity : 0.006 0.071 1488 Dihedral : 5.483 45.593 1189 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.47 % Allowed : 12.00 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.08 (0.26), residues: 1071 helix: -2.95 (0.61), residues: 40 sheet: 0.98 (0.25), residues: 429 loop : -0.62 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 114 HIS 0.009 0.001 HIS A 519 PHE 0.024 0.002 PHE A 391 TYR 0.016 0.002 TYR L 141 ARG 0.010 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 405 CYS cc_start: 0.4100 (t) cc_final: 0.3860 (t) REVERT: H 160 TYR cc_start: 0.6322 (p90) cc_final: 0.6015 (p90) REVERT: M 64 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7251 (mmtm) outliers start: 22 outliers final: 8 residues processed: 107 average time/residue: 1.2869 time to fit residues: 146.3941 Evaluate side-chains 93 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN H 219 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8487 Z= 0.229 Angle : 0.651 16.655 11553 Z= 0.335 Chirality : 0.046 0.195 1290 Planarity : 0.005 0.070 1488 Dihedral : 5.332 44.276 1189 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.68 % Allowed : 13.93 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.06 (0.27), residues: 1071 helix: -2.90 (0.63), residues: 40 sheet: 1.03 (0.25), residues: 430 loop : -0.64 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 450 HIS 0.007 0.001 HIS A 519 PHE 0.016 0.002 PHE N 141 TYR 0.015 0.002 TYR L 141 ARG 0.009 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.5114 (m-80) REVERT: H 160 TYR cc_start: 0.6313 (p90) cc_final: 0.5970 (p90) REVERT: M 64 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7264 (mmtm) outliers start: 24 outliers final: 8 residues processed: 107 average time/residue: 1.1713 time to fit residues: 134.1511 Evaluate side-chains 93 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 188 TYR Chi-restraints excluded: chain N residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 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 219 ASN M 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8487 Z= 0.218 Angle : 0.650 14.366 11553 Z= 0.335 Chirality : 0.045 0.179 1290 Planarity : 0.005 0.068 1488 Dihedral : 5.261 42.534 1189 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.64 % Allowed : 14.04 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.05 (0.27), residues: 1071 helix: -2.87 (0.64), residues: 40 sheet: 1.08 (0.26), residues: 410 loop : -0.62 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 450 HIS 0.006 0.001 HIS A 519 PHE 0.026 0.002 PHE A 391 TYR 0.016 0.002 TYR L 141 ARG 0.010 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5298 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: A 405 CYS cc_start: 0.4000 (t) cc_final: 0.3687 (t) REVERT: H 160 TYR cc_start: 0.6288 (p90) cc_final: 0.5922 (p90) REVERT: M 64 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7231 (mmtm) REVERT: N 144 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6664 (ttt-90) outliers start: 33 outliers final: 16 residues processed: 117 average time/residue: 1.1275 time to fit residues: 141.2802 Evaluate side-chains 101 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 144 ARG Chi-restraints excluded: chain N residue 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN M 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 8487 Z= 0.506 Angle : 0.838 19.881 11553 Z= 0.439 Chirality : 0.052 0.221 1290 Planarity : 0.007 0.078 1488 Dihedral : 6.339 49.955 1189 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.32 % Allowed : 16.40 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.58 (0.26), residues: 1071 helix: -3.20 (0.61), residues: 40 sheet: 0.63 (0.24), residues: 441 loop : -0.99 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 169 HIS 0.009 0.001 HIS A 519 PHE 0.026 0.003 PHE A 391 TYR 0.027 0.003 TYR L 141 ARG 0.010 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 400 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7985 (mmmm) REVERT: H 88 ASP cc_start: 0.7142 (p0) cc_final: 0.6789 (p0) REVERT: H 160 TYR cc_start: 0.6227 (p90) cc_final: 0.5936 (p90) REVERT: M 64 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7326 (mmtm) REVERT: N 144 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6730 (ttt-90) outliers start: 30 outliers final: 20 residues processed: 116 average time/residue: 1.2055 time to fit residues: 149.4559 Evaluate side-chains 111 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 144 ARG Chi-restraints excluded: chain N residue 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8487 Z= 0.212 Angle : 0.678 16.782 11553 Z= 0.349 Chirality : 0.046 0.195 1290 Planarity : 0.006 0.076 1488 Dihedral : 5.474 43.890 1189 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.75 % Allowed : 17.15 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.30 (0.26), residues: 1071 helix: -3.04 (0.62), residues: 40 sheet: 0.88 (0.25), residues: 410 loop : -0.76 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 450 HIS 0.005 0.001 HIS A 519 PHE 0.017 0.001 PHE A 388 TYR 0.017 0.002 TYR L 141 ARG 0.012 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5329 (OUTLIER) cc_final: 0.4998 (m-80) REVERT: A 405 CYS cc_start: 0.3995 (t) cc_final: 0.3714 (t) REVERT: H 88 ASP cc_start: 0.7045 (p0) cc_final: 0.6773 (p0) REVERT: H 116 ASP cc_start: 0.5484 (OUTLIER) cc_final: 0.5227 (m-30) REVERT: H 160 TYR cc_start: 0.6386 (p90) cc_final: 0.6097 (p90) REVERT: M 64 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7296 (mmtm) REVERT: N 144 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6581 (ttt-90) outliers start: 34 outliers final: 15 residues processed: 116 average time/residue: 1.1315 time to fit residues: 140.8310 Evaluate side-chains 106 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 144 ARG Chi-restraints excluded: chain N residue 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN M 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8487 Z= 0.219 Angle : 0.680 15.165 11553 Z= 0.347 Chirality : 0.046 0.172 1290 Planarity : 0.006 0.072 1488 Dihedral : 5.291 42.157 1189 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.00 % Allowed : 18.54 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.21 (0.26), residues: 1071 helix: -2.90 (0.65), residues: 40 sheet: 0.96 (0.26), residues: 405 loop : -0.71 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 450 HIS 0.005 0.001 HIS A 519 PHE 0.015 0.001 PHE A 391 TYR 0.018 0.002 TYR N 142 ARG 0.013 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5402 (OUTLIER) cc_final: 0.5080 (m-80) REVERT: A 405 CYS cc_start: 0.4009 (t) cc_final: 0.3726 (t) REVERT: H 160 TYR cc_start: 0.6387 (p90) cc_final: 0.6122 (p90) REVERT: M 64 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7243 (mmtm) REVERT: N 144 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6560 (ttt-90) outliers start: 27 outliers final: 18 residues processed: 109 average time/residue: 1.1253 time to fit residues: 131.5129 Evaluate side-chains 107 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 144 ARG Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain N residue 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 0.0370 chunk 57 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.0770 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 100 optimal weight: 0.0030 overall best weight: 0.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8487 Z= 0.173 Angle : 0.649 13.358 11553 Z= 0.330 Chirality : 0.045 0.180 1290 Planarity : 0.005 0.073 1488 Dihedral : 4.858 46.211 1189 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.82 % Allowed : 19.72 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: 0.03 (0.27), residues: 1071 helix: -2.80 (0.68), residues: 40 sheet: 1.20 (0.26), residues: 410 loop : -0.61 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 118 HIS 0.003 0.001 HIS A 519 PHE 0.016 0.001 PHE M 131 TYR 0.020 0.001 TYR N 142 ARG 0.013 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6296 (p90) cc_final: 0.6051 (p90) REVERT: M 64 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7138 (tptm) REVERT: N 138 LEU cc_start: 0.7003 (mt) cc_final: 0.6767 (mp) outliers start: 16 outliers final: 6 residues processed: 101 average time/residue: 1.1497 time to fit residues: 124.3240 Evaluate side-chains 87 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8487 Z= 0.228 Angle : 0.711 17.585 11553 Z= 0.364 Chirality : 0.046 0.181 1290 Planarity : 0.006 0.074 1488 Dihedral : 5.102 46.516 1189 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.39 % Allowed : 21.22 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.01 (0.27), residues: 1071 helix: -2.95 (0.64), residues: 40 sheet: 1.09 (0.25), residues: 425 loop : -0.61 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.005 0.001 HIS A 519 PHE 0.020 0.002 PHE N 118 TYR 0.023 0.002 TYR N 142 ARG 0.013 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6376 (p90) cc_final: 0.6102 (p90) REVERT: N 172 ASP cc_start: 0.6613 (p0) cc_final: 0.6292 (p0) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 1.2385 time to fit residues: 125.6047 Evaluate side-chains 88 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.148704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.124038 restraints weight = 22234.814| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.43 r_work: 0.3865 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8487 Z= 0.224 Angle : 0.690 11.683 11553 Z= 0.354 Chirality : 0.046 0.197 1290 Planarity : 0.006 0.073 1488 Dihedral : 5.101 46.836 1189 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.50 % Allowed : 21.22 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: 0.00 (0.27), residues: 1071 helix: -2.91 (0.66), residues: 40 sheet: 1.10 (0.25), residues: 427 loop : -0.61 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 450 HIS 0.005 0.001 HIS A 519 PHE 0.025 0.002 PHE M 131 TYR 0.022 0.002 TYR N 142 ARG 0.013 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.19 seconds wall clock time: 66 minutes 15.64 seconds (3975.64 seconds total)