Starting phenix.real_space_refine on Wed Jul 1 23:42:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sww_25487/07_2026/7sww_25487.map" } resolution = 3.13 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= 0.001 sd= 0.022 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 13 5.16 5 C 2670 2.51 5 N 674 2.21 5 O 815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 4172 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2272 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 106} 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: "C" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.01, per 1000 atoms: 0.24 Number of scatterers: 4172 At special positions: 0 Unit cell: (71.5, 93.5, 95.7, 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 13 16.00 O 815 8.00 N 674 7.00 C 2670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 401 " - " ASN A 17 " " NAG A 402 " - " ASN A 61 " " NAG A 403 " - " ASN A 125 " " NAG A 404 " - " ASN A 149 " " NAG B 1 " - " ASN A 165 " " NAG C 1 " - " ASN A 234 " Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 95.5 milliseconds 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 10 sheets defined 3.1% alpha, 44.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.468A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.881A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.537A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.070A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.913A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.544A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.141A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA L 90 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN L 43 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS L 51 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.526A pdb=" N TYR L 31 " --> pdb=" O LYS L 36 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 139 hydrogen bonds defined for protein. 360 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: 0.56 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1281 1.34 - 1.46: 1010 1.46 - 1.58: 1976 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 4283 Sorted by residual: bond pdb=" N TYR A 145 " pdb=" CA TYR A 145 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.26e-02 6.30e+03 4.06e+00 bond pdb=" C ARG H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.25e-02 6.40e+03 3.44e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CG LEU L 52 " pdb=" CD2 LEU L 52 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 ... (remaining 4278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 5602 1.79 - 3.58: 205 3.58 - 5.37: 17 5.37 - 7.16: 6 7.16 - 8.95: 2 Bond angle restraints: 5832 Sorted by residual: angle pdb=" N LEU L 53 " pdb=" CA LEU L 53 " pdb=" C LEU L 53 " ideal model delta sigma weight residual 110.42 103.86 6.56 1.55e+00 4.16e-01 1.79e+01 angle pdb=" N TYR A 170 " pdb=" CA TYR A 170 " pdb=" C TYR A 170 " ideal model delta sigma weight residual 108.69 114.58 -5.89 1.77e+00 3.19e-01 1.11e+01 angle pdb=" CA GLN L 95 " pdb=" CB GLN L 95 " pdb=" CG GLN L 95 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 121.65 -8.95 3.00e+00 1.11e-01 8.89e+00 angle pdb=" CA GLU L 61 " pdb=" CB GLU L 61 " pdb=" CG GLU L 61 " ideal model delta sigma weight residual 114.10 120.02 -5.92 2.00e+00 2.50e-01 8.76e+00 ... (remaining 5827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2193 17.88 - 35.75: 192 35.75 - 53.62: 39 53.62 - 71.50: 11 71.50 - 89.37: 2 Dihedral angle restraints: 2437 sinusoidal: 948 harmonic: 1489 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 54.66 38.34 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA TRP A 152 " pdb=" C TRP A 152 " pdb=" N MET A 153 " pdb=" CA MET A 153 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEU A 212 " pdb=" C LEU A 212 " pdb=" N VAL A 213 " pdb=" CA VAL A 213 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 2434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 636 0.121 - 0.243: 20 0.243 - 0.364: 1 0.364 - 0.485: 0 0.485 - 0.606: 1 Chirality restraints: 658 Sorted by residual: chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.19e+00 chirality pdb=" C1 NAG A 403 " pdb=" ND2 ASN A 125 " pdb=" C2 NAG A 403 " pdb=" O5 NAG A 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 655 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " -0.351 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A 403 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " -0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " -0.018 2.00e-02 2.50e+03 1.77e-02 3.91e+00 pdb=" CG ASN A 17 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 209 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.024 5.00e-02 4.00e+02 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 484 2.75 - 3.29: 3922 3.29 - 3.83: 6774 3.83 - 4.36: 7610 4.36 - 4.90: 13639 Nonbonded interactions: 32429 Sorted by model distance: nonbonded pdb=" OH TYR A 248 " pdb=" O SER A 256 " model vdw 2.217 3.040 nonbonded pdb=" O TYR A 145 " pdb=" OH TYR H 102 " model vdw 2.286 3.040 nonbonded pdb=" NH2 ARG H 98 " pdb=" OD2 ASP H 106 " model vdw 2.351 3.120 nonbonded pdb=" NH1 ARG A 273 " pdb=" OD2 ASP A 290 " model vdw 2.372 3.120 nonbonded pdb=" NZ LYS A 147 " pdb=" O TYR H 32 " model vdw 2.420 3.120 ... (remaining 32424 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.130 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.800 Find NCS groups from input model: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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 : 0.004 0.049 4296 Z= 0.181 Angle : 0.801 13.327 5866 Z= 0.421 Chirality : 0.057 0.606 658 Planarity : 0.012 0.302 734 Dihedral : 14.278 89.373 1472 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 16.07 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.48 (0.35), residues: 503 helix: 0.25 (1.34), residues: 16 sheet: 1.03 (0.36), residues: 203 loop : -1.46 (0.31), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 246 TYR 0.029 0.002 TYR L 55 PHE 0.025 0.002 PHE A 168 TRP 0.025 0.003 TRP H 50 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 4283) covalent geometry : angle 0.76443 / 0.41 ( 5832) SS BOND : bond 0.00361 / 0.22 ( 5) SS BOND : angle 0.98080 / 0.59 ( 10) hydrogen bonds : bond 0.24138 / 16.97 ( 132) hydrogen bonds : angle 10.60565 / 7.12 ( 360) link_BETA1-4 : bond 0.00543 / 0.27 ( 2) link_BETA1-4 : angle 1.34844 / 0.78 ( 6) link_NAG-ASN : bond 0.00476 / 0.26 ( 6) link_NAG-ASN : angle 4.29921 / 2.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8344 (t60) cc_final: 0.7706 (t60) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0569 time to fit residues: 5.1154 Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 ASN ** L 95 GLN ** 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 = 0.4412 r_free = 0.4412 target = 0.195852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157012 restraints weight = 6297.419| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.87 r_work: 0.3843 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4296 Z= 0.170 Angle : 0.649 6.325 5866 Z= 0.348 Chirality : 0.048 0.266 658 Planarity : 0.005 0.043 734 Dihedral : 6.406 70.548 558 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.56 % Allowed : 15.62 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.63 (0.35), residues: 503 helix: -0.04 (1.36), residues: 16 sheet: 0.70 (0.35), residues: 213 loop : -1.42 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.016 0.002 TYR A 279 PHE 0.015 0.002 PHE A 133 TRP 0.017 0.002 TRP H 47 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 4283) covalent geometry : angle 0.63552 / 0.35 ( 5832) SS BOND : bond 0.00312 / 0.20 ( 5) SS BOND : angle 0.60726 / 0.39 ( 10) hydrogen bonds : bond 0.04336 / 3.04 ( 132) hydrogen bonds : angle 7.97773 / 5.39 ( 360) link_BETA1-4 : bond 0.00303 / 0.16 ( 2) link_BETA1-4 : angle 0.83041 / 0.60 ( 6) link_NAG-ASN : bond 0.00400 / 0.25 ( 6) link_NAG-ASN : angle 2.47186 / 1.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.6691 (mptt) cc_final: 0.6462 (mptt) REVERT: H 47 TRP cc_start: 0.8344 (t60) cc_final: 0.7848 (t60) REVERT: L 27 GLN cc_start: 0.7699 (mp10) cc_final: 0.7348 (mp10) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.0559 time to fit residues: 5.2936 Evaluate side-chains 69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 ASN ** L 95 GLN ** 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 = 0.4408 r_free = 0.4408 target = 0.195356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.156559 restraints weight = 6272.860| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.85 r_work: 0.3845 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4296 Z= 0.144 Angle : 0.592 5.267 5866 Z= 0.317 Chirality : 0.045 0.219 658 Planarity : 0.004 0.043 734 Dihedral : 6.240 71.824 558 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.35 % Allowed : 16.74 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.67 (0.35), residues: 503 helix: -0.13 (1.34), residues: 16 sheet: 0.58 (0.35), residues: 212 loop : -1.34 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.020 0.002 TYR A 170 PHE 0.016 0.002 PHE H 27 TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4283) covalent geometry : angle 0.58505 / 0.32 ( 5832) SS BOND : bond 0.00245 / 0.15 ( 5) SS BOND : angle 0.64250 / 0.49 ( 10) hydrogen bonds : bond 0.03890 / 2.75 ( 132) hydrogen bonds : angle 7.30738 / 4.95 ( 360) link_BETA1-4 : bond 0.00379 / 0.19 ( 2) link_BETA1-4 : angle 0.80985 / 0.60 ( 6) link_NAG-ASN : bond 0.00332 / 0.19 ( 6) link_NAG-ASN : angle 1.72475 / 1.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7305 (m100) cc_final: 0.7091 (m100) REVERT: A 278 LYS cc_start: 0.6677 (mptt) cc_final: 0.6152 (mptt) REVERT: H 5 GLN cc_start: 0.7095 (tp-100) cc_final: 0.6857 (tp-100) outliers start: 15 outliers final: 13 residues processed: 78 average time/residue: 0.0573 time to fit residues: 5.7669 Evaluate side-chains 79 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 49 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 ASN ** L 95 GLN ** 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 = 0.4408 r_free = 0.4408 target = 0.195427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.156501 restraints weight = 6192.531| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.83 r_work: 0.3842 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4296 Z= 0.140 Angle : 0.575 7.055 5866 Z= 0.305 Chirality : 0.045 0.190 658 Planarity : 0.004 0.041 734 Dihedral : 6.112 73.503 558 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.12 % Allowed : 18.30 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.70 (0.35), residues: 503 helix: 1.14 (1.71), residues: 10 sheet: 0.43 (0.35), residues: 213 loop : -1.28 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.017 0.002 TYR A 170 PHE 0.013 0.002 PHE A 133 TRP 0.015 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4283) covalent geometry : angle 0.56844 / 0.30 ( 5832) SS BOND : bond 0.00195 / 0.12 ( 5) SS BOND : angle 0.64905 / 0.48 ( 10) hydrogen bonds : bond 0.03557 / 2.50 ( 132) hydrogen bonds : angle 7.03338 / 4.76 ( 360) link_BETA1-4 : bond 0.00396 / 0.20 ( 2) link_BETA1-4 : angle 0.85555 / 0.64 ( 6) link_NAG-ASN : bond 0.00310 / 0.19 ( 6) link_NAG-ASN : angle 1.58754 / 0.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7199 (m100) cc_final: 0.6954 (m100) REVERT: A 244 LEU cc_start: 0.8159 (mt) cc_final: 0.7959 (mt) REVERT: A 278 LYS cc_start: 0.6704 (mptt) cc_final: 0.5295 (tttt) REVERT: H 5 GLN cc_start: 0.7081 (tp-100) cc_final: 0.6790 (tp-100) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.0513 time to fit residues: 5.3033 Evaluate side-chains 79 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 ASN ** L 95 GLN ** 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 = 0.4401 r_free = 0.4401 target = 0.194884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155681 restraints weight = 6224.557| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.86 r_work: 0.3832 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4296 Z= 0.143 Angle : 0.562 4.966 5866 Z= 0.300 Chirality : 0.045 0.182 658 Planarity : 0.004 0.042 734 Dihedral : 6.043 75.505 558 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.79 % Allowed : 17.86 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.72 (0.35), residues: 503 helix: 1.18 (1.64), residues: 10 sheet: 0.34 (0.34), residues: 213 loop : -1.22 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.017 0.002 TYR A 170 PHE 0.013 0.002 PHE A 106 TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4283) covalent geometry : angle 0.55629 / 0.30 ( 5832) SS BOND : bond 0.00180 / 0.10 ( 5) SS BOND : angle 0.63121 / 0.41 ( 10) hydrogen bonds : bond 0.03379 / 2.41 ( 132) hydrogen bonds : angle 6.79022 / 4.59 ( 360) link_BETA1-4 : bond 0.00407 / 0.21 ( 2) link_BETA1-4 : angle 0.83793 / 0.63 ( 6) link_NAG-ASN : bond 0.00293 / 0.18 ( 6) link_NAG-ASN : angle 1.52830 / 0.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7214 (m100) cc_final: 0.6961 (m100) REVERT: A 278 LYS cc_start: 0.6711 (mptt) cc_final: 0.5249 (tttt) REVERT: H 5 GLN cc_start: 0.7130 (tp-100) cc_final: 0.6854 (tp-100) outliers start: 17 outliers final: 15 residues processed: 83 average time/residue: 0.0416 time to fit residues: 4.5431 Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.195086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.156831 restraints weight = 6370.868| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.82 r_work: 0.3845 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4296 Z= 0.134 Angle : 0.556 5.024 5866 Z= 0.295 Chirality : 0.044 0.192 658 Planarity : 0.004 0.040 734 Dihedral : 5.972 76.104 558 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.69 % Allowed : 17.86 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.72 (0.35), residues: 503 helix: 1.33 (1.69), residues: 10 sheet: 0.31 (0.34), residues: 213 loop : -1.20 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.016 0.001 TYR A 265 PHE 0.012 0.002 PHE H 27 TRP 0.013 0.002 TRP L 56 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4283) covalent geometry : angle 0.54967 / 0.29 ( 5832) SS BOND : bond 0.00193 / 0.11 ( 5) SS BOND : angle 0.68611 / 0.49 ( 10) hydrogen bonds : bond 0.03285 / 2.32 ( 132) hydrogen bonds : angle 6.66543 / 4.50 ( 360) link_BETA1-4 : bond 0.00460 / 0.23 ( 2) link_BETA1-4 : angle 0.86833 / 0.64 ( 6) link_NAG-ASN : bond 0.00389 / 0.22 ( 6) link_NAG-ASN : angle 1.57133 / 0.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7207 (m100) cc_final: 0.6989 (m100) REVERT: A 278 LYS cc_start: 0.6702 (mptt) cc_final: 0.5257 (tttt) REVERT: H 5 GLN cc_start: 0.7134 (tp-100) cc_final: 0.6840 (tp-100) REVERT: L 85 LYS cc_start: 0.1003 (OUTLIER) cc_final: 0.0363 (mmtt) outliers start: 21 outliers final: 18 residues processed: 82 average time/residue: 0.0474 time to fit residues: 5.1581 Evaluate side-chains 84 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 85 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.0670 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS L 33 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.195274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157210 restraints weight = 6335.414| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.82 r_work: 0.3845 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4296 Z= 0.117 Angle : 0.541 4.906 5866 Z= 0.286 Chirality : 0.044 0.181 658 Planarity : 0.004 0.037 734 Dihedral : 5.854 76.108 558 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.46 % Allowed : 18.53 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.73 (0.35), residues: 503 helix: 1.31 (1.65), residues: 10 sheet: 0.30 (0.34), residues: 213 loop : -1.20 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.015 0.001 TYR A 265 PHE 0.012 0.002 PHE H 27 TRP 0.012 0.001 TRP H 50 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 4283) covalent geometry : angle 0.53369 / 0.28 ( 5832) SS BOND : bond 0.00140 / 0.08 ( 5) SS BOND : angle 0.45051 / 0.31 ( 10) hydrogen bonds : bond 0.03125 / 2.20 ( 132) hydrogen bonds : angle 6.47914 / 4.36 ( 360) link_BETA1-4 : bond 0.00392 / 0.20 ( 2) link_BETA1-4 : angle 0.87462 / 0.61 ( 6) link_NAG-ASN : bond 0.00288 / 0.17 ( 6) link_NAG-ASN : angle 1.60436 / 0.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7186 (m100) cc_final: 0.6902 (m100) REVERT: A 277 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7414 (mp) REVERT: A 278 LYS cc_start: 0.6699 (mptt) cc_final: 0.5270 (tttt) REVERT: H 5 GLN cc_start: 0.7134 (tp-100) cc_final: 0.6851 (tp-100) REVERT: L 85 LYS cc_start: 0.1168 (OUTLIER) cc_final: 0.0547 (mmtt) outliers start: 20 outliers final: 17 residues processed: 82 average time/residue: 0.0484 time to fit residues: 5.2570 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 85 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.0060 chunk 49 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** L 95 GLN ** 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 = 0.4411 r_free = 0.4411 target = 0.195336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157405 restraints weight = 6260.983| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.80 r_work: 0.3850 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4296 Z= 0.119 Angle : 0.548 8.112 5866 Z= 0.286 Chirality : 0.044 0.181 658 Planarity : 0.004 0.037 734 Dihedral : 5.791 76.211 558 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.24 % Allowed : 19.42 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.71 (0.36), residues: 503 helix: 1.28 (1.60), residues: 10 sheet: 0.31 (0.34), residues: 214 loop : -1.19 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.016 0.001 TYR A 265 PHE 0.013 0.002 PHE H 27 TRP 0.012 0.001 TRP H 50 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4283) covalent geometry : angle 0.54195 / 0.28 ( 5832) SS BOND : bond 0.00131 / 0.08 ( 5) SS BOND : angle 0.46994 / 0.35 ( 10) hydrogen bonds : bond 0.03149 / 2.22 ( 132) hydrogen bonds : angle 6.35418 / 4.27 ( 360) link_BETA1-4 : bond 0.00359 / 0.18 ( 2) link_BETA1-4 : angle 0.86079 / 0.60 ( 6) link_NAG-ASN : bond 0.00281 / 0.16 ( 6) link_NAG-ASN : angle 1.51278 / 0.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7152 (m100) cc_final: 0.6932 (m100) REVERT: A 277 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 278 LYS cc_start: 0.6692 (mptt) cc_final: 0.5276 (tttt) REVERT: H 5 GLN cc_start: 0.7159 (tp-100) cc_final: 0.6875 (tp-100) REVERT: L 85 LYS cc_start: 0.1222 (OUTLIER) cc_final: 0.0674 (mmtt) outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 0.0499 time to fit residues: 5.3741 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 85 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.1980 chunk 38 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS L 33 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.193940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.155531 restraints weight = 6332.488| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.84 r_work: 0.3847 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4296 Z= 0.119 Angle : 0.548 6.992 5866 Z= 0.287 Chirality : 0.044 0.171 658 Planarity : 0.004 0.037 734 Dihedral : 5.785 76.157 558 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.02 % Allowed : 20.09 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.70 (0.36), residues: 503 helix: 1.37 (1.59), residues: 10 sheet: 0.30 (0.34), residues: 214 loop : -1.17 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.016 0.001 TYR A 265 PHE 0.024 0.002 PHE A 135 TRP 0.032 0.002 TRP H 47 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4283) covalent geometry : angle 0.54188 / 0.29 ( 5832) SS BOND : bond 0.00142 / 0.08 ( 5) SS BOND : angle 0.46579 / 0.34 ( 10) hydrogen bonds : bond 0.03099 / 2.20 ( 132) hydrogen bonds : angle 6.23718 / 4.21 ( 360) link_BETA1-4 : bond 0.00339 / 0.17 ( 2) link_BETA1-4 : angle 0.86675 / 0.60 ( 6) link_NAG-ASN : bond 0.00283 / 0.16 ( 6) link_NAG-ASN : angle 1.49577 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7125 (m100) cc_final: 0.6903 (m100) REVERT: A 277 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7429 (mp) REVERT: A 278 LYS cc_start: 0.6691 (mptt) cc_final: 0.5272 (tttt) REVERT: H 5 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6864 (tp-100) REVERT: L 85 LYS cc_start: 0.1212 (OUTLIER) cc_final: 0.0662 (mmtt) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.0434 time to fit residues: 4.3043 Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** L 95 GLN ** 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 = 0.4405 r_free = 0.4405 target = 0.194701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.156766 restraints weight = 6166.351| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.80 r_work: 0.3844 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4296 Z= 0.132 Angle : 0.551 6.816 5866 Z= 0.291 Chirality : 0.044 0.169 658 Planarity : 0.004 0.037 734 Dihedral : 5.809 76.462 558 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.24 % Allowed : 20.09 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.70 (0.36), residues: 503 helix: 1.68 (1.66), residues: 10 sheet: 0.32 (0.34), residues: 212 loop : -1.19 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.016 0.001 TYR A 265 PHE 0.018 0.002 PHE A 135 TRP 0.025 0.002 TRP H 47 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4283) covalent geometry : angle 0.54543 / 0.29 ( 5832) SS BOND : bond 0.00143 / 0.08 ( 5) SS BOND : angle 0.50915 / 0.40 ( 10) hydrogen bonds : bond 0.03165 / 2.25 ( 132) hydrogen bonds : angle 6.21951 / 4.20 ( 360) link_BETA1-4 : bond 0.00407 / 0.20 ( 2) link_BETA1-4 : angle 0.87630 / 0.63 ( 6) link_NAG-ASN : bond 0.00259 / 0.16 ( 6) link_NAG-ASN : angle 1.51469 / 0.91 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7459 (mp) REVERT: A 278 LYS cc_start: 0.6701 (mptt) cc_final: 0.5259 (tttt) REVERT: H 5 GLN cc_start: 0.7175 (tp-100) cc_final: 0.6882 (tp-100) REVERT: L 85 LYS cc_start: 0.1266 (OUTLIER) cc_final: 0.0651 (mmtt) REVERT: L 96 GLN cc_start: 0.7093 (pp30) cc_final: 0.6870 (pp30) outliers start: 19 outliers final: 16 residues processed: 81 average time/residue: 0.0449 time to fit residues: 4.7784 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** L 95 GLN ** 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 = 0.4393 r_free = 0.4393 target = 0.192737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.154382 restraints weight = 6232.663| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.81 r_work: 0.3828 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4296 Z= 0.162 Angle : 0.570 6.788 5866 Z= 0.302 Chirality : 0.044 0.179 658 Planarity : 0.004 0.036 734 Dihedral : 5.909 77.157 558 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.24 % Allowed : 20.98 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.81 (0.36), residues: 503 helix: 1.52 (1.73), residues: 10 sheet: 0.19 (0.34), residues: 217 loop : -1.24 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.018 0.002 TYR A 265 PHE 0.020 0.002 PHE A 135 TRP 0.021 0.002 TRP H 47 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 4283) covalent geometry : angle 0.56380 / 0.30 ( 5832) SS BOND : bond 0.00197 / 0.10 ( 5) SS BOND : angle 0.82268 / 0.65 ( 10) hydrogen bonds : bond 0.03380 / 2.40 ( 132) hydrogen bonds : angle 6.28817 / 4.25 ( 360) link_BETA1-4 : bond 0.00392 / 0.20 ( 2) link_BETA1-4 : angle 0.84091 / 0.61 ( 6) link_NAG-ASN : bond 0.00273 / 0.16 ( 6) link_NAG-ASN : angle 1.55671 / 0.93 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1161.79 seconds wall clock time: 20 minutes 29.05 seconds (1229.05 seconds total)