Starting phenix.real_space_refine on Sat Aug 23 08:48:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpu_34944/08_2025/8hpu_34944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpu_34944/08_2025/8hpu_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_34944/08_2025/8hpu_34944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpu_34944/08_2025/8hpu_34944.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpu_34944/08_2025/8hpu_34944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpu_34944/08_2025/8hpu_34944.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.61, per 1000 atoms: 0.32 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: 0.72 Conformation dependent library (CDL) restraints added in 350.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.37 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: 1.59 Time building geometry restraints manager: 0.94 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: 12.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.160 Find NCS groups from input model: 0.090 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:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.020 ------------------------------------------------------------------------------- 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 8502 Z= 0.148 Angle : 0.708 15.572 11584 Z= 0.372 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 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 ARG 0.003 0.000 ARG A 369 TYR 0.018 0.002 TYR L 174 PHE 0.017 0.001 PHE A 391 TRP 0.013 0.001 TRP N 150 HIS 0.010 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8487) covalent geometry : angle 0.69191 (11553) SS BOND : bond 0.00491 ( 14) SS BOND : angle 3.16265 ( 28) hydrogen bonds : bond 0.10302 ( 313) hydrogen bonds : angle 7.39353 ( 879) link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 0.79650 ( 3) *********************** 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 : 0.242 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: 0.7026 time to fit residues: 98.3164 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 : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN N 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.147940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.123123 restraints weight = 21786.731| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.23 r_work: 0.3870 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8502 Z= 0.166 Angle : 0.692 15.497 11584 Z= 0.356 Chirality : 0.046 0.188 1290 Planarity : 0.006 0.067 1488 Dihedral : 5.596 47.347 1189 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.61 % Allowed : 9.97 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1071 helix: -2.97 (0.61), residues: 40 sheet: 0.90 (0.25), residues: 430 loop : -0.64 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 18 TYR 0.015 0.002 TYR L 174 PHE 0.013 0.001 PHE N 141 TRP 0.007 0.001 TRP L 149 HIS 0.009 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8487) covalent geometry : angle 0.67764 (11553) SS BOND : bond 0.00681 ( 14) SS BOND : angle 2.92568 ( 28) hydrogen bonds : bond 0.03527 ( 313) hydrogen bonds : angle 6.24661 ( 879) link_NAG-ASN : bond 0.00273 ( 1) link_NAG-ASN : angle 1.47653 ( 3) *********************** 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 108 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 PHE cc_start: 0.7937 (t80) cc_final: 0.7582 (t80) REVERT: A 405 CYS cc_start: 0.4869 (t) cc_final: 0.4640 (t) REVERT: H 116 ASP cc_start: 0.6285 (OUTLIER) cc_final: 0.6080 (m-30) REVERT: H 160 TYR cc_start: 0.6457 (p90) cc_final: 0.5911 (p90) REVERT: N 18 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.7376 (mtp180) outliers start: 14 outliers final: 4 residues processed: 103 average time/residue: 0.5693 time to fit residues: 62.2712 Evaluate side-chains 84 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 199 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.146939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.122445 restraints weight = 32631.031| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.05 r_work: 0.3804 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8502 Z= 0.197 Angle : 0.719 17.923 11584 Z= 0.370 Chirality : 0.048 0.236 1290 Planarity : 0.006 0.075 1488 Dihedral : 5.710 47.338 1189 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.68 % Allowed : 11.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.26), residues: 1071 helix: -3.03 (0.59), residues: 40 sheet: 0.86 (0.25), residues: 428 loop : -0.67 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 371 TYR 0.017 0.002 TYR L 141 PHE 0.022 0.002 PHE N 141 TRP 0.006 0.001 TRP A 450 HIS 0.009 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8487) covalent geometry : angle 0.70318 (11553) SS BOND : bond 0.00689 ( 14) SS BOND : angle 3.08379 ( 28) hydrogen bonds : bond 0.03612 ( 313) hydrogen bonds : angle 6.18642 ( 879) link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 1.68579 ( 3) *********************** 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 117 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6451 (p90) cc_final: 0.5890 (p90) REVERT: M 64 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7788 (mmtm) outliers start: 24 outliers final: 11 residues processed: 109 average time/residue: 0.5657 time to fit residues: 65.5452 Evaluate side-chains 98 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 19 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 151 VAL 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 138 LEU Chi-restraints excluded: chain N residue 199 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 84 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.147017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.122764 restraints weight = 18297.778| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.05 r_work: 0.3868 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8502 Z= 0.182 Angle : 0.708 17.971 11584 Z= 0.364 Chirality : 0.047 0.240 1290 Planarity : 0.006 0.075 1488 Dihedral : 5.628 46.297 1189 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.86 % Allowed : 13.18 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.26), residues: 1071 helix: -3.00 (0.61), residues: 40 sheet: 0.89 (0.25), residues: 422 loop : -0.71 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.018 0.002 TYR L 141 PHE 0.020 0.002 PHE A 391 TRP 0.007 0.001 TRP A 450 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8487) covalent geometry : angle 0.69074 (11553) SS BOND : bond 0.00645 ( 14) SS BOND : angle 3.19434 ( 28) hydrogen bonds : bond 0.03504 ( 313) hydrogen bonds : angle 6.10157 ( 879) link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 1.63158 ( 3) *********************** 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 126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.5331 (m-80) REVERT: A 391 PHE cc_start: 0.8134 (t80) cc_final: 0.7918 (t80) REVERT: A 408 ASN cc_start: 0.7345 (p0) cc_final: 0.6963 (p0) REVERT: H 19 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7552 (m) REVERT: H 88 ASP cc_start: 0.7270 (p0) cc_final: 0.7048 (p0) REVERT: H 160 TYR cc_start: 0.6462 (p90) cc_final: 0.5909 (p90) REVERT: L 135 CYS cc_start: 0.3827 (OUTLIER) cc_final: 0.3581 (p) REVERT: M 64 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7811 (mmtm) outliers start: 35 outliers final: 15 residues processed: 121 average time/residue: 0.4741 time to fit residues: 61.2527 Evaluate side-chains 102 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 19 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 191 VAL 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 188 TYR Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.148484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.125832 restraints weight = 24676.357| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.55 r_work: 0.3857 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8502 Z= 0.125 Angle : 0.646 15.436 11584 Z= 0.331 Chirality : 0.045 0.171 1290 Planarity : 0.005 0.069 1488 Dihedral : 5.207 43.305 1189 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.75 % Allowed : 14.47 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.26), residues: 1071 helix: -2.92 (0.63), residues: 40 sheet: 1.07 (0.26), residues: 405 loop : -0.63 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.013 0.001 TYR L 141 PHE 0.022 0.001 PHE A 391 TRP 0.009 0.001 TRP A 450 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8487) covalent geometry : angle 0.63289 (11553) SS BOND : bond 0.00509 ( 14) SS BOND : angle 2.71792 ( 28) hydrogen bonds : bond 0.03078 ( 313) hydrogen bonds : angle 5.69024 ( 879) link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.48674 ( 3) *********************** 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 127 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: A 405 CYS cc_start: 0.4972 (t) cc_final: 0.4716 (t) REVERT: A 408 ASN cc_start: 0.7490 (p0) cc_final: 0.7079 (p0) REVERT: H 19 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7505 (m) REVERT: H 116 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5755 (m-30) REVERT: H 160 TYR cc_start: 0.6471 (p90) cc_final: 0.5878 (p90) REVERT: M 64 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7842 (mmtm) REVERT: N 144 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6945 (ttt-90) outliers start: 34 outliers final: 15 residues processed: 120 average time/residue: 0.5048 time to fit residues: 64.9318 Evaluate side-chains 105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 19 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 219 ASN 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 179 LEU Chi-restraints excluded: chain M residue 191 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.147248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.122512 restraints weight = 22219.052| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.41 r_work: 0.3833 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8502 Z= 0.175 Angle : 0.710 17.715 11584 Z= 0.366 Chirality : 0.046 0.216 1290 Planarity : 0.006 0.072 1488 Dihedral : 5.479 42.867 1189 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.54 % Allowed : 16.29 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.26), residues: 1071 helix: -2.89 (0.64), residues: 40 sheet: 0.97 (0.25), residues: 409 loop : -0.68 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.018 0.002 TYR L 141 PHE 0.019 0.002 PHE A 391 TRP 0.007 0.001 TRP A 450 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8487) covalent geometry : angle 0.69161 (11553) SS BOND : bond 0.00636 ( 14) SS BOND : angle 3.33699 ( 28) hydrogen bonds : bond 0.03443 ( 313) hydrogen bonds : angle 5.91147 ( 879) link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 1.49238 ( 3) *********************** 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 123 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 408 ASN cc_start: 0.7565 (p0) cc_final: 0.7157 (p0) REVERT: H 19 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7547 (m) REVERT: H 88 ASP cc_start: 0.7021 (p0) cc_final: 0.6645 (p0) REVERT: H 160 TYR cc_start: 0.6492 (p90) cc_final: 0.5948 (p90) REVERT: L 171 ASP cc_start: 0.6242 (t0) cc_final: 0.5891 (p0) REVERT: M 64 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (mmtm) REVERT: N 4 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7582 (tpp) REVERT: N 144 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7044 (ttt-90) outliers start: 32 outliers final: 18 residues processed: 115 average time/residue: 0.5407 time to fit residues: 66.1920 Evaluate side-chains 104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 19 THR 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 H residue 219 ASN 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 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 4 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN M 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.147580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.123032 restraints weight = 30659.256| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.99 r_work: 0.3818 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8502 Z= 0.163 Angle : 0.702 16.575 11584 Z= 0.360 Chirality : 0.046 0.198 1290 Planarity : 0.006 0.071 1488 Dihedral : 5.420 42.144 1189 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.97 % Allowed : 17.04 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.26), residues: 1071 helix: -2.92 (0.64), residues: 40 sheet: 0.96 (0.25), residues: 411 loop : -0.70 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.019 0.002 TYR L 141 PHE 0.022 0.002 PHE A 391 TRP 0.008 0.001 TRP A 450 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8487) covalent geometry : angle 0.68518 (11553) SS BOND : bond 0.00572 ( 14) SS BOND : angle 3.14555 ( 28) hydrogen bonds : bond 0.03299 ( 313) hydrogen bonds : angle 5.82458 ( 879) link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.36442 ( 3) *********************** 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 127 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 CYS cc_start: 0.4785 (t) cc_final: 0.4535 (t) REVERT: H 19 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7486 (m) REVERT: H 160 TYR cc_start: 0.6523 (p90) cc_final: 0.6069 (p90) REVERT: L 171 ASP cc_start: 0.6101 (t0) cc_final: 0.5781 (p0) REVERT: M 35 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8303 (m110) REVERT: M 64 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7818 (mmtm) REVERT: N 144 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7018 (ttt-90) outliers start: 36 outliers final: 23 residues processed: 118 average time/residue: 0.5205 time to fit residues: 65.7697 Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 19 THR 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 H residue 219 ASN Chi-restraints excluded: chain H residue 226 VAL 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 22 CYS Chi-restraints excluded: chain M residue 35 ASN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.147660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.122968 restraints weight = 32715.578| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.23 r_work: 0.3804 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8502 Z= 0.152 Angle : 0.695 15.756 11584 Z= 0.355 Chirality : 0.046 0.181 1290 Planarity : 0.006 0.073 1488 Dihedral : 5.378 47.487 1189 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.07 % Allowed : 17.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.26), residues: 1071 helix: -2.88 (0.65), residues: 40 sheet: 0.98 (0.25), residues: 410 loop : -0.73 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.019 0.002 TYR N 142 PHE 0.019 0.002 PHE A 388 TRP 0.008 0.001 TRP H 114 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8487) covalent geometry : angle 0.67958 (11553) SS BOND : bond 0.00517 ( 14) SS BOND : angle 2.98838 ( 28) hydrogen bonds : bond 0.03231 ( 313) hydrogen bonds : angle 5.71207 ( 879) link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 1.27186 ( 3) *********************** 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 125 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7464 (m) REVERT: H 160 TYR cc_start: 0.6528 (p90) cc_final: 0.6084 (p90) REVERT: L 168 ASP cc_start: 0.7074 (m-30) cc_final: 0.6844 (m-30) REVERT: L 171 ASP cc_start: 0.5984 (t0) cc_final: 0.5696 (p0) REVERT: N 144 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6975 (ttt-90) outliers start: 37 outliers final: 24 residues processed: 116 average time/residue: 0.4866 time to fit residues: 60.4535 Evaluate side-chains 111 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 226 VAL 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 22 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.121913 restraints weight = 33143.039| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.17 r_work: 0.3794 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8502 Z= 0.205 Angle : 0.749 15.954 11584 Z= 0.385 Chirality : 0.048 0.245 1290 Planarity : 0.006 0.076 1488 Dihedral : 5.604 44.008 1189 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.75 % Allowed : 18.33 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.26), residues: 1071 helix: -2.97 (0.63), residues: 40 sheet: 0.82 (0.25), residues: 426 loop : -0.77 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 24 TYR 0.023 0.002 TYR L 141 PHE 0.025 0.002 PHE A 391 TRP 0.012 0.001 TRP H 114 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8487) covalent geometry : angle 0.73526 (11553) SS BOND : bond 0.00647 ( 14) SS BOND : angle 2.99244 ( 28) hydrogen bonds : bond 0.03563 ( 313) hydrogen bonds : angle 5.98477 ( 879) link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 1.34695 ( 3) *********************** 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 124 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 CYS cc_start: 0.4620 (t) cc_final: 0.4346 (t) REVERT: H 19 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7578 (m) REVERT: H 88 ASP cc_start: 0.7230 (p0) cc_final: 0.6599 (p0) REVERT: H 90 GLU cc_start: 0.7584 (pp20) cc_final: 0.7279 (pm20) REVERT: H 160 TYR cc_start: 0.6531 (p90) cc_final: 0.6100 (p90) REVERT: L 171 ASP cc_start: 0.6190 (t0) cc_final: 0.5877 (p0) REVERT: N 144 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6997 (ttt-90) outliers start: 34 outliers final: 22 residues processed: 113 average time/residue: 0.5086 time to fit residues: 61.4564 Evaluate side-chains 109 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 19 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 226 VAL 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 22 CYS 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 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 102 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN M 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.148210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123652 restraints weight = 22327.752| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.24 r_work: 0.3878 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8502 Z= 0.133 Angle : 0.707 17.175 11584 Z= 0.359 Chirality : 0.046 0.225 1290 Planarity : 0.005 0.071 1488 Dihedral : 5.232 41.216 1189 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.89 % Allowed : 19.19 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.27), residues: 1071 helix: -2.89 (0.65), residues: 40 sheet: 0.96 (0.25), residues: 426 loop : -0.66 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.023 0.001 TYR N 142 PHE 0.016 0.001 PHE A 391 TRP 0.009 0.001 TRP A 450 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8487) covalent geometry : angle 0.68945 (11553) SS BOND : bond 0.00536 ( 14) SS BOND : angle 3.21246 ( 28) hydrogen bonds : bond 0.03127 ( 313) hydrogen bonds : angle 5.62005 ( 879) link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 1.23271 ( 3) ********************** 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 116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: H 19 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7612 (m) REVERT: H 88 ASP cc_start: 0.6925 (p0) cc_final: 0.6480 (p0) REVERT: H 90 GLU cc_start: 0.7486 (pp20) cc_final: 0.7188 (pm20) REVERT: H 160 TYR cc_start: 0.6552 (p90) cc_final: 0.6103 (p90) REVERT: L 162 GLU cc_start: 0.5940 (tm-30) cc_final: 0.5558 (tm-30) REVERT: L 171 ASP cc_start: 0.6074 (t0) cc_final: 0.5778 (p0) REVERT: L 191 LYS cc_start: 0.5350 (tppt) cc_final: 0.4133 (tppt) REVERT: M 35 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8170 (m110) REVERT: N 144 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6847 (ttt-90) outliers start: 26 outliers final: 19 residues processed: 110 average time/residue: 0.4869 time to fit residues: 57.3152 Evaluate side-chains 108 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 226 VAL 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 35 ASN Chi-restraints excluded: chain M residue 104 LEU 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 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 60 optimal weight: 0.0870 chunk 76 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.148747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.124114 restraints weight = 24689.408| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.62 r_work: 0.3855 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8502 Z= 0.128 Angle : 0.707 16.805 11584 Z= 0.359 Chirality : 0.046 0.257 1290 Planarity : 0.006 0.075 1488 Dihedral : 5.186 46.982 1189 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.36 % Allowed : 20.15 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.27), residues: 1071 helix: -2.95 (0.64), residues: 40 sheet: 1.02 (0.25), residues: 426 loop : -0.60 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.023 0.001 TYR N 142 PHE 0.025 0.002 PHE A 391 TRP 0.026 0.001 TRP L 149 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8487) covalent geometry : angle 0.68962 (11553) SS BOND : bond 0.00507 ( 14) SS BOND : angle 3.22624 ( 28) hydrogen bonds : bond 0.03067 ( 313) hydrogen bonds : angle 5.48634 ( 879) link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 1.19398 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.05 seconds wall clock time: 75 minutes 5.47 seconds (4505.47 seconds total)