Starting phenix.real_space_refine on Wed Jul 1 23:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_25267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_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 { model { file = "/net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_25267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_25267.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_25267.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_25267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_25267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sod_25267/07_2026/7sod_25267.map" } resolution = 3.2 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= -0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} 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 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 chiralities: 5 Time building chain proxies: 0.88, per 1000 atoms: 0.23 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: 0.29 Conformation dependent library (CDL) restraints added in 122.3 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: 0.08 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: 0.38 Time building geometry restraints manager: 0.40 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: 2103 12.77 - 25.53: 99 25.53 - 38.29: 23 38.29 - 51.06: 10 51.06 - 63.82: 8 Dihedral angle restraints: 2243 sinusoidal: 867 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 2240 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: 11.900 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.580 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 3938 Z= 0.608 Angle : 1.253 10.221 5363 Z= 0.831 Chirality : 0.076 0.330 605 Planarity : 0.005 0.026 669 Dihedral : 9.291 63.823 1346 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG L 61 TYR 0.024 0.004 TYR A 269 PHE 0.015 0.003 PHE A 55 TRP 0.022 0.004 TRP H 47 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.01108 / 0.60 ( 3926) covalent geometry : angle 1.24357 / 0.83 ( 5332) SS BOND : bond 0.00654 / 0.44 ( 5) SS BOND : angle 2.78480 / 1.53 ( 10) hydrogen bonds : bond 0.16005 / 11.48 ( 148) hydrogen bonds : angle 9.02307 / 6.36 ( 387) link_BETA1-4 : bond 0.05222 / 2.75 ( 1) link_BETA1-4 : angle 2.70978 / 1.43 ( 3) link_NAG-ASN : bond 0.05655 / 2.86 ( 6) link_NAG-ASN : angle 2.11432 / 1.30 ( 18) *********************** 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 : 0.143 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: 0.0818 time to fit residues: 6.0831 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 : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN ** A 121 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 = 0.3131 r_free = 0.3131 target = 0.111448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.090634 restraints weight = 4344.195| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.46 r_work: 0.2718 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3938 Z= 0.153 Angle : 0.569 7.577 5363 Z= 0.292 Chirality : 0.045 0.152 605 Planarity : 0.004 0.030 669 Dihedral : 4.552 17.763 511 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.40), residues: 457 helix: 1.95 (1.72), residues: 11 sheet: 1.25 (0.35), residues: 220 loop : 0.56 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.017 0.002 TYR A 265 PHE 0.013 0.002 PHE L 73 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 3926) covalent geometry : angle 0.55927 / 0.29 ( 5332) SS BOND : bond 0.00347 / 0.21 ( 5) SS BOND : angle 0.70383 / 0.40 ( 10) hydrogen bonds : bond 0.03551 / 2.51 ( 148) hydrogen bonds : angle 6.28973 / 4.44 ( 387) link_BETA1-4 : bond 0.00774 / 0.41 ( 1) link_BETA1-4 : angle 1.13143 / 0.54 ( 3) link_NAG-ASN : bond 0.00350 / 0.19 ( 6) link_NAG-ASN : angle 1.86588 / 1.21 ( 18) *********************** 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 : 0.137 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.8958 (mmm) cc_final: 0.8299 (mmm) REVERT: A 108 THR cc_start: 0.8868 (p) cc_final: 0.8621 (p) REVERT: A 177 MET cc_start: 0.6764 (mpp) cc_final: 0.5572 (mmt) REVERT: A 207 HIS cc_start: 0.8446 (t-170) cc_final: 0.7304 (m170) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.0794 time to fit residues: 4.4836 Evaluate side-chains 43 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3066 r_free = 0.3066 target = 0.105096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.082046 restraints weight = 4387.648| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.64 r_work: 0.2592 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 3938 Z= 0.246 Angle : 0.609 5.879 5363 Z= 0.318 Chirality : 0.048 0.164 605 Planarity : 0.005 0.028 669 Dihedral : 4.739 16.499 511 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.98 % Allowed : 4.90 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.39), residues: 457 helix: 2.66 (1.63), residues: 11 sheet: 1.06 (0.34), residues: 220 loop : 0.42 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.019 0.002 TYR A 265 PHE 0.017 0.002 PHE L 98 TRP 0.020 0.002 TRP H 47 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.25 ( 3926) covalent geometry : angle 0.60329 / 0.32 ( 5332) SS BOND : bond 0.00351 / 0.26 ( 5) SS BOND : angle 0.94899 / 0.54 ( 10) hydrogen bonds : bond 0.03963 / 2.84 ( 148) hydrogen bonds : angle 6.02820 / 4.25 ( 387) link_BETA1-4 : bond 0.00047 / 0.02 ( 1) link_BETA1-4 : angle 0.33110 / 0.19 ( 3) link_NAG-ASN : bond 0.00262 / 0.15 ( 6) link_NAG-ASN : angle 1.52936 / 1.06 ( 18) *********************** 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 : 0.132 Fit side-chains REVERT: L 54 MET cc_start: 0.8277 (mmm) cc_final: 0.7990 (mmm) REVERT: A 177 MET cc_start: 0.6759 (mpp) cc_final: 0.5799 (mmm) REVERT: A 187 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7695 (mtmm) REVERT: A 207 HIS cc_start: 0.8477 (t-170) cc_final: 0.7071 (m170) REVERT: A 273 ARG cc_start: 0.8597 (mmt180) cc_final: 0.8322 (mtt180) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0805 time to fit residues: 4.2898 Evaluate side-chains 44 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 13 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3088 r_free = 0.3088 target = 0.107056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.085570 restraints weight = 4375.590| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.52 r_work: 0.2643 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3938 Z= 0.140 Angle : 0.501 5.101 5363 Z= 0.262 Chirality : 0.044 0.155 605 Planarity : 0.004 0.026 669 Dihedral : 4.454 16.424 511 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.25 % Allowed : 6.62 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.40), residues: 457 helix: 2.94 (1.67), residues: 11 sheet: 1.04 (0.34), residues: 220 loop : 0.52 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.017 0.001 TYR A 265 PHE 0.012 0.002 PHE H 50 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 3926) covalent geometry : angle 0.49470 / 0.26 ( 5332) SS BOND : bond 0.00181 / 0.13 ( 5) SS BOND : angle 0.41626 / 0.24 ( 10) hydrogen bonds : bond 0.03125 / 2.25 ( 148) hydrogen bonds : angle 5.70216 / 4.02 ( 387) link_BETA1-4 : bond 0.00339 / 0.18 ( 1) link_BETA1-4 : angle 0.50758 / 0.27 ( 3) link_NAG-ASN : bond 0.00338 / 0.17 ( 6) link_NAG-ASN : angle 1.49931 / 1.00 ( 18) *********************** 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 42 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.164 Fit side-chains REVERT: A 207 HIS cc_start: 0.8461 (t-170) cc_final: 0.7135 (m170) REVERT: A 273 ARG cc_start: 0.8609 (mmt180) cc_final: 0.8345 (mtt180) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.0887 time to fit residues: 4.5382 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 : 0.135 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.105117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.083066 restraints weight = 4426.311| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.54 r_work: 0.2608 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3938 Z= 0.214 Angle : 0.556 6.261 5363 Z= 0.288 Chirality : 0.046 0.166 605 Planarity : 0.004 0.027 669 Dihedral : 4.554 18.802 511 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.49 % Allowed : 7.11 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.40), residues: 457 helix: 3.06 (1.69), residues: 11 sheet: 0.90 (0.35), residues: 211 loop : 0.48 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 102 TYR 0.019 0.002 TYR A 265 PHE 0.014 0.002 PHE A 133 TRP 0.017 0.002 TRP H 47 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.21 ( 3926) covalent geometry : angle 0.55147 / 0.29 ( 5332) SS BOND : bond 0.00305 / 0.23 ( 5) SS BOND : angle 0.54769 / 0.31 ( 10) hydrogen bonds : bond 0.03515 / 2.52 ( 148) hydrogen bonds : angle 5.68908 / 4.00 ( 387) link_BETA1-4 : bond 0.00220 / 0.12 ( 1) link_BETA1-4 : angle 0.68599 / 0.39 ( 3) link_NAG-ASN : bond 0.00110 / 0.08 ( 6) link_NAG-ASN : angle 1.31724 / 0.94 ( 18) *********************** 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 40 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.098 Fit side-chains REVERT: A 177 MET cc_start: 0.7068 (mpp) cc_final: 0.5860 (mmm) REVERT: A 207 HIS cc_start: 0.8462 (t-170) cc_final: 0.7192 (m170) REVERT: A 273 ARG cc_start: 0.8696 (mmt180) cc_final: 0.8487 (mtt180) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.0906 time to fit residues: 4.2105 Evaluate side-chains 38 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.112600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.086706 restraints weight = 4375.716| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.97 r_work: 0.2887 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3938 Z= 0.124 Angle : 0.483 5.415 5363 Z= 0.252 Chirality : 0.043 0.154 605 Planarity : 0.004 0.028 669 Dihedral : 4.362 20.518 511 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.40), residues: 457 helix: 2.99 (1.68), residues: 11 sheet: 0.93 (0.36), residues: 211 loop : 0.48 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.016 0.001 TYR A 265 PHE 0.011 0.001 PHE H 50 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.12 ( 3926) covalent geometry : angle 0.47846 / 0.25 ( 5332) SS BOND : bond 0.00188 / 0.13 ( 5) SS BOND : angle 0.27955 / 0.16 ( 10) hydrogen bonds : bond 0.02941 / 2.11 ( 148) hydrogen bonds : angle 5.51156 / 3.87 ( 387) link_BETA1-4 : bond 0.00345 / 0.18 ( 1) link_BETA1-4 : angle 0.57625 / 0.31 ( 3) link_NAG-ASN : bond 0.00159 / 0.08 ( 6) link_NAG-ASN : angle 1.25457 / 0.88 ( 18) *********************** 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 39 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.136 Fit side-chains REVERT: A 177 MET cc_start: 0.7027 (mpp) cc_final: 0.5885 (mmm) REVERT: A 207 HIS cc_start: 0.8478 (t-170) cc_final: 0.7188 (m90) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1104 time to fit residues: 5.1220 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 : 0.150 ------------------------------------------------------------------------------- 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 30 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110050 restraints weight = 4167.730| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.93 r_work: 0.2647 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3938 Z= 0.145 Angle : 0.495 5.850 5363 Z= 0.258 Chirality : 0.044 0.160 605 Planarity : 0.004 0.026 669 Dihedral : 4.298 17.764 511 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.74 % Allowed : 7.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.40), residues: 457 helix: 3.02 (1.68), residues: 11 sheet: 0.93 (0.36), residues: 211 loop : 0.53 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.017 0.001 TYR A 265 PHE 0.012 0.002 PHE H 50 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 3926) covalent geometry : angle 0.49009 / 0.26 ( 5332) SS BOND : bond 0.00208 / 0.15 ( 5) SS BOND : angle 0.39703 / 0.23 ( 10) hydrogen bonds : bond 0.03038 / 2.18 ( 148) hydrogen bonds : angle 5.45434 / 3.83 ( 387) link_BETA1-4 : bond 0.00223 / 0.12 ( 1) link_BETA1-4 : angle 0.61008 / 0.34 ( 3) link_NAG-ASN : bond 0.00166 / 0.08 ( 6) link_NAG-ASN : angle 1.26952 / 0.89 ( 18) *********************** 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: 3 poor density : 37 time to evaluate : 0.134 Fit side-chains REVERT: L 54 MET cc_start: 0.8457 (mmm) cc_final: 0.8044 (mmm) REVERT: A 177 MET cc_start: 0.6853 (mpp) cc_final: 0.5724 (mmm) REVERT: A 207 HIS cc_start: 0.8454 (t-170) cc_final: 0.7097 (m90) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.0897 time to fit residues: 4.3427 Evaluate side-chains 38 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER 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 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.112061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.086076 restraints weight = 4349.663| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.98 r_work: 0.3013 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3938 Z= 0.153 Angle : 0.497 5.792 5363 Z= 0.259 Chirality : 0.044 0.161 605 Planarity : 0.004 0.027 669 Dihedral : 4.293 16.200 511 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.74 % Allowed : 7.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.41), residues: 457 helix: 2.97 (1.69), residues: 11 sheet: 0.89 (0.36), residues: 211 loop : 0.53 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 102 TYR 0.017 0.001 TYR A 265 PHE 0.012 0.002 PHE H 50 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.15 ( 3926) covalent geometry : angle 0.49220 / 0.26 ( 5332) SS BOND : bond 0.00210 / 0.15 ( 5) SS BOND : angle 0.40179 / 0.23 ( 10) hydrogen bonds : bond 0.03024 / 2.17 ( 148) hydrogen bonds : angle 5.43569 / 3.81 ( 387) link_BETA1-4 : bond 0.00260 / 0.14 ( 1) link_BETA1-4 : angle 0.68474 / 0.38 ( 3) link_NAG-ASN : bond 0.00152 / 0.08 ( 6) link_NAG-ASN : angle 1.26545 / 0.89 ( 18) *********************** 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 37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.134 Fit side-chains REVERT: A 177 MET cc_start: 0.6992 (mpp) cc_final: 0.5832 (mmm) REVERT: A 207 HIS cc_start: 0.8481 (t-170) cc_final: 0.7199 (m90) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.0772 time to fit residues: 3.4276 Evaluate side-chains 36 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.112032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.086258 restraints weight = 4341.125| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.93 r_work: 0.2641 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3938 Z= 0.153 Angle : 0.497 5.864 5363 Z= 0.259 Chirality : 0.044 0.161 605 Planarity : 0.004 0.026 669 Dihedral : 4.275 15.709 511 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.74 % Allowed : 8.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.41), residues: 457 helix: 2.98 (1.69), residues: 11 sheet: 0.86 (0.36), residues: 211 loop : 0.55 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.017 0.001 TYR A 265 PHE 0.012 0.002 PHE A 133 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.15 ( 3926) covalent geometry : angle 0.49208 / 0.26 ( 5332) SS BOND : bond 0.00210 / 0.15 ( 5) SS BOND : angle 0.40996 / 0.23 ( 10) hydrogen bonds : bond 0.03038 / 2.18 ( 148) hydrogen bonds : angle 5.41915 / 3.80 ( 387) link_BETA1-4 : bond 0.00231 / 0.12 ( 1) link_BETA1-4 : angle 0.69800 / 0.39 ( 3) link_NAG-ASN : bond 0.00163 / 0.08 ( 6) link_NAG-ASN : angle 1.27617 / 0.89 ( 18) *********************** 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 37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.092 Fit side-chains REVERT: H 43 LYS cc_start: 0.8223 (mptt) cc_final: 0.7949 (mttp) REVERT: A 177 MET cc_start: 0.6809 (mpp) cc_final: 0.5726 (mmm) REVERT: A 207 HIS cc_start: 0.8483 (t-170) cc_final: 0.7149 (m90) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.0593 time to fit residues: 2.7742 Evaluate side-chains 35 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.087851 restraints weight = 4366.904| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.94 r_work: 0.2656 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3938 Z= 0.109 Angle : 0.462 5.361 5363 Z= 0.242 Chirality : 0.043 0.153 605 Planarity : 0.004 0.027 669 Dihedral : 4.122 15.334 511 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.74 % Allowed : 8.33 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.41), residues: 457 helix: 2.93 (1.69), residues: 11 sheet: 0.87 (0.36), residues: 211 loop : 0.59 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.015 0.001 TYR A 265 PHE 0.010 0.001 PHE H 50 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 3926) covalent geometry : angle 0.45704 / 0.24 ( 5332) SS BOND : bond 0.00153 / 0.11 ( 5) SS BOND : angle 0.33008 / 0.19 ( 10) hydrogen bonds : bond 0.02735 / 1.97 ( 148) hydrogen bonds : angle 5.30662 / 3.72 ( 387) link_BETA1-4 : bond 0.00316 / 0.17 ( 1) link_BETA1-4 : angle 0.68967 / 0.37 ( 3) link_NAG-ASN : bond 0.00191 / 0.09 ( 6) link_NAG-ASN : angle 1.24284 / 0.87 ( 18) ********************** 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 40 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.147 Fit side-chains REVERT: L 54 MET cc_start: 0.8473 (mmm) cc_final: 0.8127 (mmm) REVERT: L 61 ARG cc_start: 0.7949 (ptt-90) cc_final: 0.7643 (ptt-90) REVERT: H 43 LYS cc_start: 0.8169 (mptt) cc_final: 0.7911 (mttp) REVERT: A 177 MET cc_start: 0.6816 (mpp) cc_final: 0.5778 (mmt) REVERT: A 207 HIS cc_start: 0.8488 (t-170) cc_final: 0.7140 (m170) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0885 time to fit residues: 4.2039 Evaluate side-chains 39 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 22 optimal weight: 0.0470 chunk 3 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.113711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.087983 restraints weight = 4306.291| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.91 r_work: 0.2649 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3938 Z= 0.124 Angle : 0.469 5.563 5363 Z= 0.246 Chirality : 0.043 0.156 605 Planarity : 0.004 0.027 669 Dihedral : 4.104 15.397 511 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.74 % Allowed : 8.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.40), residues: 457 helix: 2.90 (1.70), residues: 11 sheet: 0.90 (0.36), residues: 206 loop : 0.49 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.016 0.001 TYR A 265 PHE 0.011 0.001 PHE A 133 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.12 ( 3926) covalent geometry : angle 0.46452 / 0.24 ( 5332) SS BOND : bond 0.00177 / 0.13 ( 5) SS BOND : angle 0.38469 / 0.22 ( 10) hydrogen bonds : bond 0.02820 / 2.03 ( 148) hydrogen bonds : angle 5.29880 / 3.71 ( 387) link_BETA1-4 : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : angle 0.71258 / 0.39 ( 3) link_NAG-ASN : bond 0.00174 / 0.08 ( 6) link_NAG-ASN : angle 1.24966 / 0.88 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1209.98 seconds wall clock time: 21 minutes 27.52 seconds (1287.52 seconds total)