Starting phenix.real_space_refine on Tue Mar 3 12:29:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sww_25487/03_2026/7sww_25487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sww_25487/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sww_25487/03_2026/7sww_25487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sww_25487/03_2026/7sww_25487.map" model { file = "/net/cci-nas-00/data/ceres_data/7sww_25487/03_2026/7sww_25487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sww_25487/03_2026/7sww_25487.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.87, per 1000 atoms: 0.21 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: 0.33 Conformation dependent library (CDL) restraints added in 146.3 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: 0.17 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: 0.61 Time building geometry restraints manager: 0.44 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: 2349 17.88 - 35.75: 200 35.75 - 53.62: 42 53.62 - 71.50: 12 71.50 - 89.37: 2 Dihedral angle restraints: 2605 sinusoidal: 1116 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 2602 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: 0.910 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.210 Find NCS groups from input model: 0.020 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: 7.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 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 : 13.913 89.373 1640 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 covalent geometry : bond 0.00385 ( 4283) covalent geometry : angle 0.76443 ( 5832) SS BOND : bond 0.00361 ( 5) SS BOND : angle 0.98080 ( 10) hydrogen bonds : bond 0.24138 ( 132) hydrogen bonds : angle 10.60565 ( 360) link_BETA1-4 : bond 0.00543 ( 2) link_BETA1-4 : angle 1.34844 ( 6) link_NAG-ASN : bond 0.00476 ( 6) link_NAG-ASN : angle 4.29921 ( 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 : 0.138 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: 0.0726 time to fit residues: 6.4508 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 : 0.149 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.195939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157062 restraints weight = 6300.561| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.87 r_work: 0.3840 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4296 Z= 0.169 Angle : 0.647 6.222 5866 Z= 0.346 Chirality : 0.048 0.260 658 Planarity : 0.005 0.042 734 Dihedral : 6.910 70.883 726 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.79 % Allowed : 15.62 % Favored : 82.59 % 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: -0.64 (0.35), residues: 503 helix: -0.05 (1.36), residues: 16 sheet: 0.68 (0.35), residues: 213 loop : -1.43 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.015 0.002 TYR A 279 PHE 0.016 0.002 PHE A 168 TRP 0.016 0.002 TRP H 47 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4283) covalent geometry : angle 0.63300 ( 5832) SS BOND : bond 0.00302 ( 5) SS BOND : angle 0.61775 ( 10) hydrogen bonds : bond 0.04445 ( 132) hydrogen bonds : angle 7.90287 ( 360) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 0.94604 ( 6) link_NAG-ASN : bond 0.00469 ( 6) link_NAG-ASN : angle 2.43157 ( 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 77 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.6705 (mptt) cc_final: 0.6438 (mptt) REVERT: H 47 TRP cc_start: 0.8345 (t60) cc_final: 0.7858 (t60) REVERT: L 27 GLN cc_start: 0.7698 (mp10) cc_final: 0.7337 (mp10) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.0617 time to fit residues: 5.9929 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS 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: 1.9990 chunk 27 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4419 r_free = 0.4419 target = 0.196273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.157340 restraints weight = 6282.120| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.89 r_work: 0.3857 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4296 Z= 0.120 Angle : 0.579 7.799 5866 Z= 0.307 Chirality : 0.045 0.225 658 Planarity : 0.004 0.040 734 Dihedral : 6.476 70.921 726 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.68 % Allowed : 17.41 % 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: -0.60 (0.35), residues: 503 helix: -0.07 (1.33), residues: 16 sheet: 0.62 (0.35), residues: 212 loop : -1.29 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 67 TYR 0.019 0.001 TYR A 170 PHE 0.018 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 covalent geometry : bond 0.00266 ( 4283) covalent geometry : angle 0.57194 ( 5832) SS BOND : bond 0.00239 ( 5) SS BOND : angle 0.64850 ( 10) hydrogen bonds : bond 0.03682 ( 132) hydrogen bonds : angle 7.11622 ( 360) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 0.88433 ( 6) link_NAG-ASN : bond 0.00348 ( 6) link_NAG-ASN : angle 1.68880 ( 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 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7184 (m100) cc_final: 0.6946 (m100) REVERT: A 244 LEU cc_start: 0.8149 (mt) cc_final: 0.7942 (mt) REVERT: A 278 LYS cc_start: 0.6657 (mptt) cc_final: 0.6142 (mptt) REVERT: H 5 GLN cc_start: 0.7057 (tp-100) cc_final: 0.6779 (tp-100) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.0604 time to fit residues: 6.0990 Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 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: 1.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4358 r_free = 0.4358 target = 0.190809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.151644 restraints weight = 6196.112| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.82 r_work: 0.3789 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 4296 Z= 0.315 Angle : 0.720 6.489 5866 Z= 0.387 Chirality : 0.051 0.295 658 Planarity : 0.005 0.049 734 Dihedral : 7.331 79.146 726 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.02 % Allowed : 16.74 % Favored : 79.24 % 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: -0.87 (0.35), residues: 503 helix: 0.51 (1.74), residues: 10 sheet: 0.29 (0.34), residues: 218 loop : -1.39 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 44 TYR 0.031 0.003 TYR A 279 PHE 0.030 0.003 PHE A 43 TRP 0.017 0.003 TRP H 50 HIS 0.009 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00725 ( 4283) covalent geometry : angle 0.71121 ( 5832) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.15300 ( 10) hydrogen bonds : bond 0.04783 ( 132) hydrogen bonds : angle 7.56005 ( 360) link_BETA1-4 : bond 0.00630 ( 2) link_BETA1-4 : angle 0.93730 ( 6) link_NAG-ASN : bond 0.00384 ( 6) link_NAG-ASN : angle 2.00294 ( 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 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7577 (m100) cc_final: 0.7335 (m100) REVERT: A 278 LYS cc_start: 0.7014 (mptt) cc_final: 0.5296 (tttt) REVERT: H 5 GLN cc_start: 0.7712 (tp-100) cc_final: 0.7457 (tp-100) REVERT: H 47 TRP cc_start: 0.8297 (t60) cc_final: 0.8051 (t60) outliers start: 18 outliers final: 15 residues processed: 81 average time/residue: 0.0591 time to fit residues: 6.3265 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 51 THR 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 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 285 ILE 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: 1.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.0270 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.194037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.155232 restraints weight = 6230.999| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.82 r_work: 0.3837 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2281 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= 0.128 Angle : 0.560 4.506 5866 Z= 0.301 Chirality : 0.045 0.204 658 Planarity : 0.004 0.043 734 Dihedral : 6.578 77.662 726 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.35 % Allowed : 20.31 % 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: -0.85 (0.35), residues: 503 helix: 1.13 (1.79), residues: 10 sheet: 0.19 (0.34), residues: 213 loop : -1.26 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.016 0.001 TYR A 265 PHE 0.013 0.002 PHE H 27 TRP 0.014 0.002 TRP L 56 HIS 0.006 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4283) covalent geometry : angle 0.55357 ( 5832) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.66981 ( 10) hydrogen bonds : bond 0.03363 ( 132) hydrogen bonds : angle 6.86748 ( 360) link_BETA1-4 : bond 0.00479 ( 2) link_BETA1-4 : angle 0.98507 ( 6) link_NAG-ASN : bond 0.00358 ( 6) link_NAG-ASN : angle 1.57487 ( 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 84 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7170 (m100) cc_final: 0.6923 (m100) REVERT: A 278 LYS cc_start: 0.6689 (mptt) cc_final: 0.5214 (tttt) REVERT: H 5 GLN cc_start: 0.7156 (tp-100) cc_final: 0.6850 (tp-100) REVERT: L 85 LYS cc_start: 0.1240 (OUTLIER) cc_final: 0.0442 (mmtt) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.0591 time to fit residues: 5.9931 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 53 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS L 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.193248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.154933 restraints weight = 6357.352| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.86 r_work: 0.3821 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4296 Z= 0.180 Angle : 0.597 6.061 5866 Z= 0.317 Chirality : 0.046 0.211 658 Planarity : 0.004 0.043 734 Dihedral : 6.660 77.852 726 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.46 % Allowed : 19.20 % 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: -0.86 (0.36), residues: 503 helix: 0.81 (1.68), residues: 10 sheet: 0.20 (0.35), residues: 218 loop : -1.29 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.019 0.002 TYR A 265 PHE 0.016 0.002 PHE A 43 TRP 0.014 0.002 TRP H 50 HIS 0.004 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 4283) covalent geometry : angle 0.59024 ( 5832) SS BOND : bond 0.00183 ( 5) SS BOND : angle 0.61286 ( 10) hydrogen bonds : bond 0.03611 ( 132) hydrogen bonds : angle 6.84440 ( 360) link_BETA1-4 : bond 0.00453 ( 2) link_BETA1-4 : angle 0.90408 ( 6) link_NAG-ASN : bond 0.00314 ( 6) link_NAG-ASN : angle 1.69242 ( 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 91 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7268 (m100) cc_final: 0.7020 (m100) REVERT: A 277 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7500 (mp) REVERT: A 278 LYS cc_start: 0.6723 (mptt) cc_final: 0.5238 (tttt) REVERT: H 5 GLN cc_start: 0.7258 (tp-100) cc_final: 0.6959 (tp-100) REVERT: L 85 LYS cc_start: 0.1173 (OUTLIER) cc_final: 0.0348 (mmtt) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.0647 time to fit residues: 6.8304 Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.0570 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.194464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156351 restraints weight = 6370.895| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.85 r_work: 0.3837 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4296 Z= 0.128 Angle : 0.560 5.431 5866 Z= 0.297 Chirality : 0.045 0.193 658 Planarity : 0.004 0.042 734 Dihedral : 6.418 77.567 726 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.02 % Allowed : 19.87 % Favored : 76.12 % 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: -0.78 (0.36), residues: 503 helix: 1.21 (1.69), residues: 10 sheet: 0.29 (0.35), residues: 213 loop : -1.26 (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 0.045 0.002 PHE A 135 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4283) covalent geometry : angle 0.55416 ( 5832) SS BOND : bond 0.00165 ( 5) SS BOND : angle 0.56732 ( 10) hydrogen bonds : bond 0.03266 ( 132) hydrogen bonds : angle 6.56305 ( 360) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 0.98598 ( 6) link_NAG-ASN : bond 0.00311 ( 6) link_NAG-ASN : angle 1.52307 ( 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 88 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7201 (m100) cc_final: 0.6902 (m100) REVERT: A 277 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7450 (mp) REVERT: A 278 LYS cc_start: 0.6731 (mptt) cc_final: 0.5220 (tttt) REVERT: H 5 GLN cc_start: 0.7206 (tp-100) cc_final: 0.6863 (tp-100) REVERT: L 85 LYS cc_start: 0.1101 (OUTLIER) cc_final: 0.0440 (mmtt) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.0653 time to fit residues: 6.8466 Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS 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 250 THR 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: 1.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.193846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155327 restraints weight = 6285.878| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.83 r_work: 0.3823 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4296 Z= 0.159 Angle : 0.576 5.184 5866 Z= 0.307 Chirality : 0.045 0.204 658 Planarity : 0.004 0.042 734 Dihedral : 6.559 77.906 726 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.02 % Allowed : 20.31 % 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: -0.77 (0.36), residues: 503 helix: 1.10 (1.68), residues: 10 sheet: 0.28 (0.35), residues: 218 loop : -1.26 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.015 0.001 TYR A 279 PHE 0.044 0.002 PHE A 135 TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4283) covalent geometry : angle 0.57003 ( 5832) SS BOND : bond 0.00181 ( 5) SS BOND : angle 0.64443 ( 10) hydrogen bonds : bond 0.03400 ( 132) hydrogen bonds : angle 6.49148 ( 360) link_BETA1-4 : bond 0.00427 ( 2) link_BETA1-4 : angle 0.92744 ( 6) link_NAG-ASN : bond 0.00304 ( 6) link_NAG-ASN : angle 1.56832 ( 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 88 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7242 (m100) cc_final: 0.7021 (m100) REVERT: A 277 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7473 (mp) REVERT: A 278 LYS cc_start: 0.6741 (mptt) cc_final: 0.5230 (tttt) REVERT: H 5 GLN cc_start: 0.7283 (tp-100) cc_final: 0.6946 (tp-100) REVERT: L 85 LYS cc_start: 0.1317 (OUTLIER) cc_final: 0.0561 (mmtt) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.0585 time to fit residues: 6.2124 Evaluate side-chains 82 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS 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 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 7 SER 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: 1.9990 chunk 38 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS 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 = 0.195701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157241 restraints weight = 6352.289| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.88 r_work: 0.3847 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4296 Z= 0.108 Angle : 0.546 7.715 5866 Z= 0.286 Chirality : 0.044 0.185 658 Planarity : 0.004 0.041 734 Dihedral : 6.232 77.166 726 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.73 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: -0.74 (0.36), residues: 503 helix: 1.62 (1.64), residues: 10 sheet: 0.29 (0.35), residues: 214 loop : -1.23 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 60 TYR 0.012 0.001 TYR A 265 PHE 0.011 0.002 PHE H 27 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4283) covalent geometry : angle 0.54047 ( 5832) SS BOND : bond 0.00118 ( 5) SS BOND : angle 0.45274 ( 10) hydrogen bonds : bond 0.03057 ( 132) hydrogen bonds : angle 6.16758 ( 360) link_BETA1-4 : bond 0.00429 ( 2) link_BETA1-4 : angle 1.06822 ( 6) link_NAG-ASN : bond 0.00312 ( 6) link_NAG-ASN : angle 1.44137 ( 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 86 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8303 (m-40) cc_final: 0.7984 (t0) REVERT: A 152 TRP cc_start: 0.7121 (m100) cc_final: 0.6896 (m100) REVERT: A 277 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 278 LYS cc_start: 0.6706 (mptt) cc_final: 0.5208 (tttt) REVERT: H 5 GLN cc_start: 0.7166 (tp-100) cc_final: 0.6870 (tp-100) REVERT: L 85 LYS cc_start: 0.1469 (OUTLIER) cc_final: 0.0854 (mmtt) outliers start: 19 outliers final: 15 residues processed: 79 average time/residue: 0.0585 time to fit residues: 6.0758 Evaluate side-chains 83 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 46 SER 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 231 ILE Chi-restraints excluded: chain A residue 250 THR 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: 0.6980 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.194063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.155682 restraints weight = 6171.205| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.81 r_work: 0.3832 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2904 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= 0.138 Angle : 0.564 6.491 5866 Z= 0.297 Chirality : 0.044 0.178 658 Planarity : 0.004 0.041 734 Dihedral : 6.368 77.330 726 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.69 % Allowed : 20.09 % Favored : 75.22 % 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: -0.76 (0.36), residues: 503 helix: 1.56 (1.64), residues: 10 sheet: 0.24 (0.35), residues: 218 loop : -1.23 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.013 0.001 TYR A 265 PHE 0.014 0.002 PHE A 135 TRP 0.013 0.002 TRP H 47 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4283) covalent geometry : angle 0.55826 ( 5832) SS BOND : bond 0.00142 ( 5) SS BOND : angle 0.49544 ( 10) hydrogen bonds : bond 0.03204 ( 132) hydrogen bonds : angle 6.22801 ( 360) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 0.96837 ( 6) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 1.50876 ( 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 88 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8287 (m-40) cc_final: 0.7993 (t0) REVERT: A 152 TRP cc_start: 0.7136 (m100) cc_final: 0.6901 (m100) REVERT: A 157 PHE cc_start: 0.7141 (t80) cc_final: 0.6908 (t80) REVERT: A 274 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7652 (t) REVERT: A 277 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 278 LYS cc_start: 0.6722 (mptt) cc_final: 0.5171 (tttt) REVERT: H 5 GLN cc_start: 0.7223 (tp-100) cc_final: 0.6924 (tp-100) REVERT: L 85 LYS cc_start: 0.1619 (OUTLIER) cc_final: 0.0918 (mmtt) outliers start: 21 outliers final: 16 residues processed: 79 average time/residue: 0.0562 time to fit residues: 5.8319 Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 46 SER 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 231 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 THR 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: 6.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.193893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155329 restraints weight = 6253.999| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.83 r_work: 0.3823 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4296 Z= 0.157 Angle : 0.581 7.072 5866 Z= 0.306 Chirality : 0.045 0.190 658 Planarity : 0.004 0.040 734 Dihedral : 6.594 78.367 726 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.24 % Allowed : 20.76 % Favored : 75.00 % 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: -0.86 (0.36), residues: 503 helix: 1.44 (1.69), residues: 10 sheet: 0.13 (0.35), residues: 218 loop : -1.25 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.014 0.001 TYR A 279 PHE 0.016 0.002 PHE A 135 TRP 0.013 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4283) covalent geometry : angle 0.57417 ( 5832) SS BOND : bond 0.00157 ( 5) SS BOND : angle 0.59531 ( 10) hydrogen bonds : bond 0.03307 ( 132) hydrogen bonds : angle 6.29926 ( 360) link_BETA1-4 : bond 0.00468 ( 2) link_BETA1-4 : angle 0.92072 ( 6) link_NAG-ASN : bond 0.00255 ( 6) link_NAG-ASN : angle 1.59734 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.74 seconds wall clock time: 23 minutes 38.41 seconds (1418.41 seconds total)