Starting phenix.real_space_refine on Tue Feb 11 03:21:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sod_25267/02_2025/7sod_25267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sod_25267/02_2025/7sod_25267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sod_25267/02_2025/7sod_25267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sod_25267/02_2025/7sod_25267.map" model { file = "/net/cci-nas-00/data/ceres_data/7sod_25267/02_2025/7sod_25267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sod_25267/02_2025/7sod_25267.cif" } resolution = 3.2 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= -0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2464 2.51 5 N 617 2.21 5 O 734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3830 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 230} Chain breaks: 5 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.89, per 1000 atoms: 1.54 Number of scatterers: 3830 At special positions: 0 Unit cell: (83.457, 70.812, 76.713, 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 15 16.00 O 734 8.00 N 617 7.00 C 2464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 17 " " NAG A1305 " - " ASN A 165 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 463.2 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 882 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 4.2% alpha, 58.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.802A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.802A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 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 10 through 12 removed outlier: 6.662A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.962A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.323A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.296A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.023A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.848A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.472A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 387 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: 1.15 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 654 1.32 - 1.45: 1111 1.45 - 1.57: 2139 1.57 - 1.70: 2 1.70 - 1.82: 20 Bond restraints: 3926 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.530 1.460 0.070 1.69e-02 3.50e+03 1.73e+01 bond pdb=" C PHE A 32 " pdb=" O PHE A 32 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.15e-02 7.56e+03 1.44e+01 bond pdb=" C TRP L 3 " pdb=" O TRP L 3 " ideal model delta sigma weight residual 1.234 1.199 0.036 1.22e-02 6.72e+03 8.64e+00 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.53e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.42e+00 ... (remaining 3921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 4900 2.04 - 4.09: 354 4.09 - 6.13: 57 6.13 - 8.18: 20 8.18 - 10.22: 1 Bond angle restraints: 5332 Sorted by residual: angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.08 -6.42 7.20e-01 1.93e+00 7.95e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.76 127.18 -7.42 1.00e+00 1.00e+00 5.50e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 126.79 -6.94 1.01e+00 9.80e-01 4.73e+01 angle pdb=" C GLY L 99 " pdb=" N PRO L 100 " pdb=" CA PRO L 100 " ideal model delta sigma weight residual 119.32 127.13 -7.81 1.14e+00 7.69e-01 4.69e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 126.77 -6.74 9.90e-01 1.02e+00 4.63e+01 ... (remaining 5327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 2235 12.77 - 25.53: 112 25.53 - 38.29: 25 38.29 - 51.06: 10 51.06 - 63.82: 8 Dihedral angle restraints: 2390 sinusoidal: 1014 harmonic: 1376 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.17 41.83 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA TYR H 95 " pdb=" C TYR H 95 " pdb=" N CYS H 96 " pdb=" CA CYS H 96 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR A 208 " pdb=" C THR A 208 " pdb=" N PRO A 209 " pdb=" CA PRO A 209 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 422 0.066 - 0.132: 139 0.132 - 0.198: 27 0.198 - 0.264: 9 0.264 - 0.330: 8 Chirality restraints: 605 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.34e+01 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C2 NAG A1305 " pdb=" C1 NAG A1305 " pdb=" C3 NAG A1305 " pdb=" N2 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 602 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 31 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C SER A 31 " -0.045 2.00e-02 2.50e+03 pdb=" O SER A 31 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 32 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 305 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C SER A 305 " 0.040 2.00e-02 2.50e+03 pdb=" O SER A 305 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 306 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 32 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C PHE A 32 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 32 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 33 " -0.012 2.00e-02 2.50e+03 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 58 2.68 - 3.24: 3365 3.24 - 3.79: 5626 3.79 - 4.35: 8285 4.35 - 4.90: 13643 Nonbonded interactions: 30977 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.129 3.040 nonbonded pdb=" O ASP L 92 " pdb=" NH1 ARG H 103 " model vdw 2.524 3.120 nonbonded pdb=" ND2 ASN A 81 " pdb=" O THR A 240 " model vdw 2.554 3.120 nonbonded pdb=" N TYR A 144 " pdb=" O TYR A 144 " model vdw 2.584 2.496 nonbonded pdb=" C SER A 31 " pdb=" OG SER A 31 " model vdw 2.601 2.616 ... (remaining 30972 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.011 0.070 3926 Z= 0.720 Angle : 1.244 10.221 5332 Z= 0.830 Chirality : 0.076 0.330 605 Planarity : 0.005 0.026 669 Dihedral : 9.166 63.823 1493 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.49 % Allowed : 0.25 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.38), residues: 457 helix: 0.51 (1.78), residues: 11 sheet: 1.07 (0.34), residues: 214 loop : 0.41 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.015 0.003 PHE A 55 TYR 0.024 0.004 TYR A 269 ARG 0.004 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.407 Fit side-chains REVERT: A 177 MET cc_start: 0.5837 (mpp) cc_final: 0.5040 (mmm) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.2455 time to fit residues: 18.0247 Evaluate side-chains 44 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.111686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.090924 restraints weight = 4267.195| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.45 r_work: 0.2722 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3926 Z= 0.226 Angle : 0.555 7.462 5332 Z= 0.288 Chirality : 0.046 0.152 605 Planarity : 0.004 0.031 669 Dihedral : 4.815 33.657 658 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.98 % Allowed : 3.92 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.40), residues: 457 helix: 1.91 (1.75), residues: 11 sheet: 1.25 (0.35), residues: 220 loop : 0.57 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.012 0.002 PHE L 98 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.8919 (mmm) cc_final: 0.8274 (mmm) REVERT: A 108 THR cc_start: 0.8864 (p) cc_final: 0.8608 (p) REVERT: A 177 MET cc_start: 0.6767 (mpp) cc_final: 0.5574 (mmt) REVERT: A 207 HIS cc_start: 0.8449 (t-170) cc_final: 0.7307 (m170) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.2299 time to fit residues: 12.9781 Evaluate side-chains 44 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN H 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.106144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.083460 restraints weight = 4339.629| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 1.60 r_work: 0.2613 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3926 Z= 0.317 Angle : 0.561 5.477 5332 Z= 0.297 Chirality : 0.046 0.160 605 Planarity : 0.004 0.028 669 Dihedral : 4.808 39.901 658 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.98 % Allowed : 4.41 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.39), residues: 457 helix: 2.78 (1.64), residues: 11 sheet: 1.10 (0.34), residues: 220 loop : 0.49 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.004 0.001 HIS A 49 PHE 0.015 0.002 PHE L 98 TYR 0.018 0.002 TYR A 265 ARG 0.004 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.419 Fit side-chains REVERT: L 54 MET cc_start: 0.8310 (mmm) cc_final: 0.7991 (mmm) REVERT: A 207 HIS cc_start: 0.8466 (t-170) cc_final: 0.7036 (m170) REVERT: A 273 ARG cc_start: 0.8571 (mmt180) cc_final: 0.8281 (mtt180) outliers start: 4 outliers final: 4 residues processed: 44 average time/residue: 0.2345 time to fit residues: 12.4450 Evaluate side-chains 46 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 16 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.108141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.085597 restraints weight = 4326.580| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.60 r_work: 0.2669 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3926 Z= 0.191 Angle : 0.480 4.844 5332 Z= 0.254 Chirality : 0.044 0.152 605 Planarity : 0.004 0.026 669 Dihedral : 4.441 35.643 658 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.49 % Allowed : 5.88 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.40), residues: 457 helix: 3.00 (1.67), residues: 11 sheet: 1.12 (0.34), residues: 220 loop : 0.60 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE H 50 TYR 0.016 0.001 TYR A 265 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.447 Fit side-chains REVERT: L 54 MET cc_start: 0.8274 (mmm) cc_final: 0.8034 (mmm) REVERT: A 177 MET cc_start: 0.6708 (mpp) cc_final: 0.5588 (mmm) REVERT: A 187 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7566 (mtmm) REVERT: A 207 HIS cc_start: 0.8445 (t-170) cc_final: 0.7062 (m170) REVERT: A 273 ARG cc_start: 0.8542 (mmt180) cc_final: 0.8305 (mtt180) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.2073 time to fit residues: 10.9439 Evaluate side-chains 41 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.105315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.083037 restraints weight = 4575.782| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.69 r_work: 0.2606 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 3926 Z= 0.385 Angle : 0.562 5.913 5332 Z= 0.293 Chirality : 0.047 0.169 605 Planarity : 0.004 0.026 669 Dihedral : 4.666 35.493 658 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.74 % Allowed : 6.37 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.40), residues: 457 helix: 3.07 (1.69), residues: 11 sheet: 0.95 (0.36), residues: 211 loop : 0.48 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.004 0.001 HIS A 49 PHE 0.015 0.002 PHE A 133 TYR 0.020 0.002 TYR A 265 ARG 0.003 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.394 Fit side-chains REVERT: A 177 MET cc_start: 0.7040 (mpp) cc_final: 0.5838 (mmm) REVERT: A 207 HIS cc_start: 0.8496 (t-170) cc_final: 0.7229 (m170) REVERT: A 273 ARG cc_start: 0.8704 (mmt180) cc_final: 0.8488 (mtt180) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.2209 time to fit residues: 10.9870 Evaluate side-chains 40 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3067 r_free = 0.3067 target = 0.106983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.083957 restraints weight = 4426.410| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.61 r_work: 0.2682 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3926 Z= 0.229 Angle : 0.489 5.233 5332 Z= 0.258 Chirality : 0.044 0.156 605 Planarity : 0.004 0.028 669 Dihedral : 4.439 33.001 658 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.25 % Allowed : 8.33 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.40), residues: 457 helix: 2.97 (1.67), residues: 11 sheet: 0.93 (0.36), residues: 211 loop : 0.50 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.012 0.002 PHE H 50 TYR 0.017 0.001 TYR A 265 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.611 Fit side-chains REVERT: A 177 MET cc_start: 0.7037 (mpp) cc_final: 0.5851 (mmm) REVERT: A 207 HIS cc_start: 0.8452 (t-170) cc_final: 0.7221 (m170) REVERT: A 273 ARG cc_start: 0.8680 (mmt180) cc_final: 0.8469 (mtt180) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.2368 time to fit residues: 11.4568 Evaluate side-chains 38 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.0170 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3074 r_free = 0.3074 target = 0.107403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.084729 restraints weight = 4462.614| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.67 r_work: 0.2637 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3926 Z= 0.219 Angle : 0.485 5.429 5332 Z= 0.256 Chirality : 0.044 0.157 605 Planarity : 0.004 0.024 669 Dihedral : 4.302 29.601 658 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.25 % Allowed : 8.58 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.40), residues: 457 helix: 2.97 (1.67), residues: 11 sheet: 0.93 (0.36), residues: 211 loop : 0.49 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.012 0.002 PHE H 50 TYR 0.017 0.001 TYR A 265 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.440 Fit side-chains REVERT: A 177 MET cc_start: 0.6998 (mpp) cc_final: 0.5837 (mmm) REVERT: A 207 HIS cc_start: 0.8452 (t-170) cc_final: 0.7208 (m90) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.2473 time to fit residues: 12.1428 Evaluate side-chains 38 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.0010 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.107946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.085301 restraints weight = 4439.628| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.67 r_work: 0.2652 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3926 Z= 0.193 Angle : 0.472 5.335 5332 Z= 0.249 Chirality : 0.043 0.156 605 Planarity : 0.004 0.027 669 Dihedral : 4.220 27.081 658 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.74 % Allowed : 8.58 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.40), residues: 457 helix: 2.95 (1.66), residues: 11 sheet: 0.94 (0.36), residues: 211 loop : 0.48 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE H 50 TYR 0.016 0.001 TYR A 265 ARG 0.004 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.422 Fit side-chains REVERT: A 177 MET cc_start: 0.6957 (mpp) cc_final: 0.5833 (mmt) REVERT: A 207 HIS cc_start: 0.8451 (t-170) cc_final: 0.7223 (m90) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.2181 time to fit residues: 9.9226 Evaluate side-chains 35 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3078 r_free = 0.3078 target = 0.107476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.084276 restraints weight = 4423.979| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.63 r_work: 0.2641 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3926 Z= 0.228 Angle : 0.485 5.683 5332 Z= 0.255 Chirality : 0.044 0.159 605 Planarity : 0.004 0.025 669 Dihedral : 4.157 25.927 658 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.49 % Allowed : 8.82 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.40), residues: 457 helix: 2.97 (1.67), residues: 11 sheet: 0.90 (0.36), residues: 211 loop : 0.47 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.012 0.002 PHE H 50 TYR 0.017 0.001 TYR A 265 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.409 Fit side-chains REVERT: H 43 LYS cc_start: 0.8236 (mptt) cc_final: 0.7946 (mttp) REVERT: A 177 MET cc_start: 0.6935 (mpp) cc_final: 0.5808 (mmt) REVERT: A 207 HIS cc_start: 0.8454 (t-170) cc_final: 0.7192 (m90) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.1997 time to fit residues: 8.6962 Evaluate side-chains 36 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.106488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.083140 restraints weight = 4492.471| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.75 r_work: 0.2621 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3926 Z= 0.285 Angle : 0.506 5.822 5332 Z= 0.266 Chirality : 0.045 0.164 605 Planarity : 0.004 0.027 669 Dihedral : 4.307 27.893 658 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.49 % Allowed : 8.82 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.40), residues: 457 helix: 2.96 (1.66), residues: 11 sheet: 0.85 (0.36), residues: 211 loop : 0.38 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.013 0.002 PHE A 133 TYR 0.018 0.001 TYR A 265 ARG 0.005 0.001 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.405 Fit side-chains REVERT: H 43 LYS cc_start: 0.8230 (mptt) cc_final: 0.7970 (mttp) REVERT: A 177 MET cc_start: 0.7024 (mpp) cc_final: 0.5870 (mmm) REVERT: A 207 HIS cc_start: 0.8438 (t-170) cc_final: 0.7160 (m170) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.2141 time to fit residues: 9.1754 Evaluate side-chains 34 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.108039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.084702 restraints weight = 4428.761| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.73 r_work: 0.2627 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3926 Z= 0.207 Angle : 0.473 5.305 5332 Z= 0.250 Chirality : 0.043 0.156 605 Planarity : 0.004 0.026 669 Dihedral : 4.153 27.239 658 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.25 % Allowed : 9.07 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.40), residues: 457 helix: 2.94 (1.66), residues: 11 sheet: 0.88 (0.36), residues: 206 loop : 0.37 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE H 50 TYR 0.016 0.001 TYR A 265 ARG 0.004 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.41 seconds wall clock time: 46 minutes 1.37 seconds (2761.37 seconds total)