Starting phenix.real_space_refine on Fri Dec 27 09:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sod_25267/12_2024/7sod_25267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sod_25267/12_2024/7sod_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_25267/12_2024/7sod_25267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sod_25267/12_2024/7sod_25267.map" model { file = "/net/cci-nas-00/data/ceres_data/7sod_25267/12_2024/7sod_25267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sod_25267/12_2024/7sod_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-5532/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: 5.94, per 1000 atoms: 1.55 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: 1.11 Conformation dependent library (CDL) restraints added in 475.1 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: 0.56 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: 1.10 Time building geometry restraints manager: 1.20 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: 9.680 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.200 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- 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 : 0.474 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: 0.2476 time to fit residues: 18.3944 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 : 0.501 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.419 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.8663 (mmm) cc_final: 0.8100 (mmm) REVERT: A 108 THR cc_start: 0.8815 (p) cc_final: 0.8597 (p) REVERT: A 177 MET cc_start: 0.6458 (mpp) cc_final: 0.5435 (mmt) REVERT: A 207 HIS cc_start: 0.7865 (t-170) cc_final: 0.7307 (m170) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.2044 time to fit residues: 11.6716 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 : 0.375 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3926 Z= 0.221 Angle : 0.508 4.908 5332 Z= 0.270 Chirality : 0.044 0.151 605 Planarity : 0.004 0.029 669 Dihedral : 4.545 37.889 658 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.74 % Allowed : 4.41 % Favored : 94.85 % 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: 1.37 (0.40), residues: 457 helix: 2.94 (1.66), residues: 11 sheet: 1.23 (0.34), residues: 220 loop : 0.58 (0.43), residues: 226 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 L 73 TYR 0.016 0.001 TYR A 265 ARG 0.005 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: 3 poor density : 43 time to evaluate : 0.435 Fit side-chains REVERT: L 54 MET cc_start: 0.7778 (mmm) cc_final: 0.7457 (mmm) REVERT: A 207 HIS cc_start: 0.7901 (t-170) cc_final: 0.7278 (m170) outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.2138 time to fit residues: 11.4720 Evaluate side-chains 45 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3926 Z= 0.308 Angle : 0.537 5.671 5332 Z= 0.281 Chirality : 0.046 0.162 605 Planarity : 0.004 0.026 669 Dihedral : 4.603 36.339 658 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.74 % Allowed : 5.39 % Favored : 93.87 % 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: 1.21 (0.40), residues: 457 helix: 2.91 (1.66), residues: 11 sheet: 1.08 (0.34), residues: 220 loop : 0.53 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.015 0.002 PHE A 133 TYR 0.018 0.002 TYR A 265 ARG 0.003 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 46 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.457 Fit side-chains REVERT: A 177 MET cc_start: 0.6743 (mpp) cc_final: 0.5709 (mmm) REVERT: A 207 HIS cc_start: 0.7944 (t-170) cc_final: 0.7338 (m170) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.2063 time to fit residues: 11.1819 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 167 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3926 Z= 0.271 Angle : 0.509 5.510 5332 Z= 0.268 Chirality : 0.045 0.159 605 Planarity : 0.004 0.026 669 Dihedral : 4.503 34.508 658 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.74 % Allowed : 6.13 % 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 (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: 1.11 (0.40), residues: 457 helix: 2.93 (1.68), residues: 11 sheet: 0.98 (0.35), residues: 211 loop : 0.53 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.004 0.001 HIS A 49 PHE 0.012 0.002 PHE H 50 TYR 0.018 0.001 TYR A 265 ARG 0.004 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 : 0.391 Fit side-chains REVERT: A 177 MET cc_start: 0.6715 (mpp) cc_final: 0.5716 (mmm) REVERT: A 207 HIS cc_start: 0.7919 (t-170) cc_final: 0.7278 (m170) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.2039 time to fit residues: 10.3871 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 : 0.431 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3926 Z= 0.346 Angle : 0.548 6.141 5332 Z= 0.286 Chirality : 0.046 0.167 605 Planarity : 0.004 0.026 669 Dihedral : 4.596 32.440 658 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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 (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: 0.98 (0.40), residues: 457 helix: 2.99 (1.69), residues: 11 sheet: 0.89 (0.35), residues: 211 loop : 0.44 (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 0.019 0.002 TYR A 265 ARG 0.003 0.001 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 41 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.441 Fit side-chains REVERT: L 54 MET cc_start: 0.7731 (mmm) cc_final: 0.7475 (mmm) REVERT: A 177 MET cc_start: 0.6770 (mpp) cc_final: 0.5780 (mmm) REVERT: A 207 HIS cc_start: 0.7917 (t-170) cc_final: 0.7267 (m170) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.2460 time to fit residues: 11.7980 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 : 0.428 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 26 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2880 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= 0.184 Angle : 0.474 5.319 5332 Z= 0.251 Chirality : 0.043 0.154 605 Planarity : 0.004 0.025 669 Dihedral : 4.310 30.032 658 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 1.05 (0.40), residues: 457 helix: 2.94 (1.69), 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 0.012 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 0.003 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 41 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.437 Fit side-chains REVERT: A 177 MET cc_start: 0.6702 (mpp) cc_final: 0.5708 (mmm) REVERT: A 207 HIS cc_start: 0.7905 (t-170) cc_final: 0.7287 (m90) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.2495 time to fit residues: 12.2183 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 : 0.431 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3926 Z= 0.332 Angle : 0.537 6.375 5332 Z= 0.281 Chirality : 0.045 0.168 605 Planarity : 0.004 0.025 669 Dihedral : 4.471 28.808 658 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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: 0.89 (0.40), residues: 457 helix: 2.99 (1.69), residues: 11 sheet: 0.83 (0.36), residues: 211 loop : 0.36 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.004 0.001 HIS A 49 PHE 0.015 0.002 PHE A 133 TYR 0.019 0.002 TYR A 265 ARG 0.004 0.001 ARG L 61 *********************** 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 34 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.443 Fit side-chains REVERT: H 43 LYS cc_start: 0.8135 (mptt) cc_final: 0.7855 (mttp) REVERT: A 177 MET cc_start: 0.6801 (mpp) cc_final: 0.5809 (mmm) REVERT: A 207 HIS cc_start: 0.7918 (t-170) cc_final: 0.7263 (m170) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.2058 time to fit residues: 8.7938 Evaluate side-chains 33 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER 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 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3926 Z= 0.260 Angle : 0.501 5.652 5332 Z= 0.263 Chirality : 0.044 0.160 605 Planarity : 0.004 0.028 669 Dihedral : 4.339 28.322 658 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 0.85 (0.40), residues: 457 helix: 2.96 (1.68), residues: 11 sheet: 0.81 (0.35), residues: 211 loop : 0.34 (0.42), 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 0.003 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 37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.392 Fit side-chains REVERT: L 54 MET cc_start: 0.7813 (mmm) cc_final: 0.7468 (mmm) REVERT: A 158 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8317 (mtp85) REVERT: A 177 MET cc_start: 0.6785 (mpp) cc_final: 0.5802 (mmm) REVERT: A 207 HIS cc_start: 0.7911 (t-170) cc_final: 0.7269 (m170) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.1874 time to fit residues: 8.8279 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 : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER 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 45 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3926 Z= 0.174 Angle : 0.464 5.309 5332 Z= 0.246 Chirality : 0.043 0.152 605 Planarity : 0.004 0.025 669 Dihedral : 4.092 26.227 658 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.93 (0.40), residues: 457 helix: 2.86 (1.67), residues: 11 sheet: 0.89 (0.35), residues: 206 loop : 0.38 (0.42), residues: 240 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 0.010 0.001 PHE H 50 TYR 0.015 0.001 TYR A 265 ARG 0.004 0.000 ARG L 61 ********************** 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 37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.440 Fit side-chains REVERT: L 54 MET cc_start: 0.7793 (mmm) cc_final: 0.7468 (mmm) REVERT: H 43 LYS cc_start: 0.8108 (mptt) cc_final: 0.7867 (mttp) REVERT: A 158 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8299 (mtp85) REVERT: A 177 MET cc_start: 0.6710 (mpp) cc_final: 0.5776 (mmt) REVERT: A 207 HIS cc_start: 0.7880 (t-170) cc_final: 0.7272 (m170) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.2022 time to fit residues: 9.4380 Evaluate side-chains 37 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.0270 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3071 r_free = 0.3071 target = 0.107025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.084678 restraints weight = 4425.065| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.64 r_work: 0.2640 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3098 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= 0.239 Angle : 0.490 5.812 5332 Z= 0.258 Chirality : 0.044 0.160 605 Planarity : 0.004 0.025 669 Dihedral : 4.154 26.533 658 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.25 % Allowed : 8.82 % 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 (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: 2.89 (1.67), residues: 11 sheet: 0.86 (0.35), residues: 206 loop : 0.38 (0.42), residues: 240 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 0.003 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.26 seconds wall clock time: 31 minutes 8.19 seconds (1868.19 seconds total)