Starting phenix.real_space_refine on Wed Jun 4 22:14:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sww_25487/06_2025/7sww_25487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sww_25487/06_2025/7sww_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_25487/06_2025/7sww_25487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sww_25487/06_2025/7sww_25487.map" model { file = "/net/cci-nas-00/data/ceres_data/7sww_25487/06_2025/7sww_25487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sww_25487/06_2025/7sww_25487.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.25, per 1000 atoms: 0.78 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: 0.91 Conformation dependent library (CDL) restraints added in 499.0 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: 0.58 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: 1.15 Time building geometry restraints manager: 1.13 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.620 Find NCS groups from input model: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (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 TRP 0.025 0.003 TRP H 50 HIS 0.005 0.002 HIS H 35 PHE 0.025 0.002 PHE A 168 TYR 0.029 0.002 TYR L 55 ARG 0.003 0.001 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 6) link_NAG-ASN : angle 4.29921 ( 18) link_BETA1-4 : bond 0.00543 ( 2) link_BETA1-4 : angle 1.34844 ( 6) hydrogen bonds : bond 0.24138 ( 132) hydrogen bonds : angle 10.60565 ( 360) SS BOND : bond 0.00361 ( 5) SS BOND : angle 0.98080 ( 10) covalent geometry : bond 0.00385 ( 4283) covalent geometry : angle 0.76443 ( 5832) *********************** 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 : 0.377 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: 0.2348 time to fit residues: 20.5887 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 : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.196120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157318 restraints weight = 6269.394| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.86 r_work: 0.3850 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4296 Z= 0.163 Angle : 0.642 6.236 5866 Z= 0.344 Chirality : 0.048 0.276 658 Planarity : 0.004 0.042 734 Dihedral : 6.890 70.045 726 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.35), residues: 503 helix: -0.04 (1.35), residues: 16 sheet: 0.71 (0.35), residues: 213 loop : -1.42 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.005 0.002 HIS H 35 PHE 0.015 0.002 PHE A 168 TYR 0.014 0.002 TYR A 279 ARG 0.002 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 6) link_NAG-ASN : angle 2.48600 ( 18) link_BETA1-4 : bond 0.00464 ( 2) link_BETA1-4 : angle 0.90582 ( 6) hydrogen bonds : bond 0.04576 ( 132) hydrogen bonds : angle 8.00575 ( 360) SS BOND : bond 0.00300 ( 5) SS BOND : angle 0.58105 ( 10) covalent geometry : bond 0.00360 ( 4283) covalent geometry : angle 0.62814 ( 5832) *********************** 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 : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8333 (t60) cc_final: 0.7847 (t60) REVERT: L 27 GLN cc_start: 0.7687 (mp10) cc_final: 0.7341 (mp10) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.1509 time to fit residues: 14.0959 Evaluate side-chains 68 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.0010 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5464 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.196411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.161397 restraints weight = 6228.993| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.03 r_work: 0.3841 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4296 Z= 0.120 Angle : 0.573 5.365 5866 Z= 0.306 Chirality : 0.045 0.229 658 Planarity : 0.004 0.041 734 Dihedral : 6.519 70.362 726 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.68 % Allowed : 17.19 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.35), residues: 503 helix: -0.07 (1.32), residues: 16 sheet: 0.61 (0.35), residues: 212 loop : -1.32 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 PHE 0.020 0.002 PHE H 27 TYR 0.019 0.001 TYR A 170 ARG 0.001 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 6) link_NAG-ASN : angle 1.71243 ( 18) link_BETA1-4 : bond 0.00553 ( 2) link_BETA1-4 : angle 0.90370 ( 6) hydrogen bonds : bond 0.03695 ( 132) hydrogen bonds : angle 7.18416 ( 360) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.54408 ( 10) covalent geometry : bond 0.00267 ( 4283) covalent geometry : angle 0.56568 ( 5832) *********************** 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 : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7252 (m100) cc_final: 0.7004 (m100) REVERT: H 5 GLN cc_start: 0.7067 (tp-100) cc_final: 0.6773 (tp-100) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.1416 time to fit residues: 13.9535 Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.0070 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.195111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159935 restraints weight = 6306.746| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.99 r_work: 0.3835 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1816 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= 0.136 Angle : 0.572 6.798 5866 Z= 0.304 Chirality : 0.045 0.209 658 Planarity : 0.004 0.041 734 Dihedral : 6.473 72.316 726 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.90 % Allowed : 17.63 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.35), residues: 503 helix: 1.57 (1.69), residues: 10 sheet: 0.44 (0.35), residues: 213 loop : -1.22 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 PHE 0.013 0.002 PHE H 27 TYR 0.016 0.001 TYR A 265 ARG 0.001 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 6) link_NAG-ASN : angle 1.61521 ( 18) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 0.85593 ( 6) hydrogen bonds : bond 0.03536 ( 132) hydrogen bonds : angle 6.98170 ( 360) SS BOND : bond 0.00235 ( 5) SS BOND : angle 0.63182 ( 10) covalent geometry : bond 0.00308 ( 4283) covalent geometry : angle 0.56501 ( 5832) *********************** 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 82 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7212 (m100) cc_final: 0.6960 (m100) REVERT: A 278 LYS cc_start: 0.6809 (mptt) cc_final: 0.5594 (mppt) REVERT: H 5 GLN cc_start: 0.7126 (tp-100) cc_final: 0.6823 (tp-100) REVERT: L 48 HIS cc_start: 0.5296 (t70) cc_final: 0.5072 (t-90) outliers start: 13 outliers final: 12 residues processed: 78 average time/residue: 0.1377 time to fit residues: 13.9817 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 : 0.429 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4408 r_free = 0.4408 target = 0.195168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159627 restraints weight = 6395.323| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.97 r_work: 0.3839 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4296 Z= 0.125 Angle : 0.544 4.907 5866 Z= 0.291 Chirality : 0.044 0.192 658 Planarity : 0.004 0.039 734 Dihedral : 6.296 74.100 726 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.79 % Allowed : 17.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.36), residues: 503 helix: 1.37 (1.66), residues: 10 sheet: 0.35 (0.34), residues: 213 loop : -1.12 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS A 245 PHE 0.013 0.002 PHE H 27 TYR 0.015 0.001 TYR A 265 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 6) link_NAG-ASN : angle 1.52213 ( 18) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 0.91711 ( 6) hydrogen bonds : bond 0.03255 ( 132) hydrogen bonds : angle 6.70067 ( 360) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.64211 ( 10) covalent geometry : bond 0.00285 ( 4283) covalent geometry : angle 0.53711 ( 5832) *********************** 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 : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7184 (m100) cc_final: 0.6905 (m100) REVERT: A 278 LYS cc_start: 0.6730 (mptt) cc_final: 0.5267 (tttt) REVERT: H 5 GLN cc_start: 0.7101 (tp-100) cc_final: 0.6826 (tp-100) REVERT: L 48 HIS cc_start: 0.5163 (t70) cc_final: 0.4959 (t-90) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.1403 time to fit residues: 15.0045 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 : 0.454 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4399 r_free = 0.4399 target = 0.194834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156258 restraints weight = 6226.683| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.81 r_work: 0.3832 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4296 Z= 0.163 Angle : 0.576 6.365 5866 Z= 0.306 Chirality : 0.045 0.209 658 Planarity : 0.004 0.038 734 Dihedral : 6.421 75.708 726 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.02 % Allowed : 18.75 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.35), residues: 503 helix: 1.12 (1.63), residues: 10 sheet: 0.26 (0.34), residues: 213 loop : -1.15 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.006 0.002 HIS A 207 PHE 0.016 0.002 PHE A 43 TYR 0.018 0.002 TYR A 265 ARG 0.002 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 6) link_NAG-ASN : angle 1.69398 ( 18) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 0.87350 ( 6) hydrogen bonds : bond 0.03458 ( 132) hydrogen bonds : angle 6.71905 ( 360) SS BOND : bond 0.00237 ( 5) SS BOND : angle 0.71071 ( 10) covalent geometry : bond 0.00374 ( 4283) covalent geometry : angle 0.56861 ( 5832) *********************** 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: 18 poor density : 73 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7215 (m100) cc_final: 0.6941 (m100) REVERT: A 278 LYS cc_start: 0.6761 (mptt) cc_final: 0.5235 (tttt) REVERT: H 5 GLN cc_start: 0.7206 (tp-100) cc_final: 0.6914 (tp-100) REVERT: L 85 LYS cc_start: 0.1074 (OUTLIER) cc_final: 0.0362 (mmtt) outliers start: 18 outliers final: 15 residues processed: 81 average time/residue: 0.1462 time to fit residues: 15.2579 Evaluate side-chains 84 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 207 HIS ** 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 = 0.4403 r_free = 0.4403 target = 0.194726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.156977 restraints weight = 6229.629| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.79 r_work: 0.3847 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2504 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= 0.123 Angle : 0.543 4.945 5866 Z= 0.289 Chirality : 0.044 0.231 658 Planarity : 0.004 0.038 734 Dihedral : 6.574 75.780 726 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.46 % Allowed : 18.97 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.36), residues: 503 helix: 1.27 (1.64), residues: 10 sheet: 0.28 (0.35), residues: 213 loop : -1.15 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 207 PHE 0.013 0.002 PHE H 27 TYR 0.016 0.001 TYR A 265 ARG 0.001 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 6) link_NAG-ASN : angle 1.52688 ( 18) link_BETA1-4 : bond 0.00466 ( 2) link_BETA1-4 : angle 0.95748 ( 6) hydrogen bonds : bond 0.03134 ( 132) hydrogen bonds : angle 6.51535 ( 360) SS BOND : bond 0.00127 ( 5) SS BOND : angle 0.51530 ( 10) covalent geometry : bond 0.00277 ( 4283) covalent geometry : angle 0.53650 ( 5832) *********************** 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: 20 poor density : 68 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7145 (m100) cc_final: 0.6874 (m100) REVERT: A 277 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7445 (mp) REVERT: A 278 LYS cc_start: 0.6745 (mptt) cc_final: 0.5255 (tttt) REVERT: H 5 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6870 (tp-100) REVERT: L 85 LYS cc_start: 0.1251 (OUTLIER) cc_final: 0.0661 (mmtt) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.1356 time to fit residues: 14.3260 Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4376 r_free = 0.4376 target = 0.192548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154267 restraints weight = 6180.302| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.81 r_work: 0.3817 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 4296 Z= 0.238 Angle : 0.636 5.568 5866 Z= 0.340 Chirality : 0.047 0.234 658 Planarity : 0.004 0.042 734 Dihedral : 6.859 77.657 726 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.46 % Allowed : 19.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.36), residues: 503 helix: 0.58 (1.73), residues: 10 sheet: 0.17 (0.34), residues: 218 loop : -1.25 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.004 0.002 HIS A 207 PHE 0.025 0.003 PHE A 43 TYR 0.024 0.002 TYR A 279 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 6) link_NAG-ASN : angle 1.85897 ( 18) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 0.83270 ( 6) hydrogen bonds : bond 0.03925 ( 132) hydrogen bonds : angle 6.82859 ( 360) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.78236 ( 10) covalent geometry : bond 0.00550 ( 4283) covalent geometry : angle 0.62779 ( 5832) *********************** 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 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7839 (mt-10) REVERT: A 278 LYS cc_start: 0.6305 (mptt) cc_final: 0.4869 (tttt) REVERT: H 5 GLN cc_start: 0.7324 (tp-100) cc_final: 0.6989 (tp-100) REVERT: L 85 LYS cc_start: 0.1178 (OUTLIER) cc_final: 0.0315 (mmtt) outliers start: 20 outliers final: 17 residues processed: 80 average time/residue: 0.1368 time to fit residues: 14.2151 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 : 0.400 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4397 r_free = 0.4397 target = 0.194399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156245 restraints weight = 6231.964| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.83 r_work: 0.3839 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2790 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= 0.124 Angle : 0.576 7.451 5866 Z= 0.304 Chirality : 0.045 0.204 658 Planarity : 0.004 0.040 734 Dihedral : 6.702 76.925 726 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.36), residues: 503 helix: 1.16 (1.69), residues: 10 sheet: 0.20 (0.35), residues: 218 loop : -1.24 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.006 0.001 HIS H 35 PHE 0.026 0.002 PHE A 135 TYR 0.015 0.001 TYR A 265 ARG 0.001 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 6) link_NAG-ASN : angle 1.63828 ( 18) link_BETA1-4 : bond 0.00415 ( 2) link_BETA1-4 : angle 0.99557 ( 6) hydrogen bonds : bond 0.03199 ( 132) hydrogen bonds : angle 6.42249 ( 360) SS BOND : bond 0.00138 ( 5) SS BOND : angle 0.42845 ( 10) covalent geometry : bond 0.00287 ( 4283) covalent geometry : angle 0.56935 ( 5832) *********************** 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 93 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.7137 (m100) cc_final: 0.6860 (m100) REVERT: A 278 LYS cc_start: 0.6713 (mptt) cc_final: 0.5243 (tttt) REVERT: H 5 GLN cc_start: 0.7195 (tp-100) cc_final: 0.6868 (tp-100) REVERT: L 85 LYS cc_start: 0.1255 (OUTLIER) cc_final: 0.0580 (mmtt) outliers start: 18 outliers final: 13 residues processed: 85 average time/residue: 0.1512 time to fit residues: 16.4496 Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4396 r_free = 0.4396 target = 0.194375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.155990 restraints weight = 6255.794| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.84 r_work: 0.3833 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4296 Z= 0.146 Angle : 0.583 7.264 5866 Z= 0.308 Chirality : 0.045 0.194 658 Planarity : 0.004 0.040 734 Dihedral : 6.712 76.565 726 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.79 % Allowed : 19.42 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.36), residues: 503 helix: 1.24 (1.68), residues: 10 sheet: 0.18 (0.35), residues: 218 loop : -1.27 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.005 0.001 HIS H 35 PHE 0.039 0.002 PHE A 135 TYR 0.014 0.001 TYR A 265 ARG 0.001 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 6) link_NAG-ASN : angle 1.56730 ( 18) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 0.96074 ( 6) hydrogen bonds : bond 0.03239 ( 132) hydrogen bonds : angle 6.37136 ( 360) SS BOND : bond 0.00128 ( 5) SS BOND : angle 0.58080 ( 10) covalent geometry : bond 0.00338 ( 4283) covalent geometry : angle 0.57697 ( 5832) ********************** 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 86 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7140 (t80) cc_final: 0.6940 (t80) REVERT: A 221 SER cc_start: 0.8477 (m) cc_final: 0.8220 (p) REVERT: A 278 LYS cc_start: 0.6727 (mptt) cc_final: 0.5216 (tttt) REVERT: H 5 GLN cc_start: 0.7255 (tp-100) cc_final: 0.6922 (tp-100) REVERT: L 85 LYS cc_start: 0.1391 (OUTLIER) cc_final: 0.0702 (mmtt) outliers start: 17 outliers final: 16 residues processed: 77 average time/residue: 0.1522 time to fit residues: 15.0545 Evaluate side-chains 86 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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 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 38 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4374 r_free = 0.4374 target = 0.192041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153489 restraints weight = 6285.643| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.85 r_work: 0.3804 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 4296 Z= 0.263 Angle : 0.660 8.034 5866 Z= 0.353 Chirality : 0.048 0.238 658 Planarity : 0.005 0.047 734 Dihedral : 7.151 77.751 726 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.36), residues: 503 helix: 0.75 (1.79), residues: 10 sheet: 0.13 (0.35), residues: 217 loop : -1.25 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 47 HIS 0.005 0.002 HIS H 35 PHE 0.046 0.003 PHE A 135 TYR 0.024 0.002 TYR L 102 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 6) link_NAG-ASN : angle 1.72691 ( 18) link_BETA1-4 : bond 0.00481 ( 2) link_BETA1-4 : angle 0.84923 ( 6) hydrogen bonds : bond 0.03951 ( 132) hydrogen bonds : angle 6.61149 ( 360) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.81537 ( 10) covalent geometry : bond 0.00610 ( 4283) covalent geometry : angle 0.65360 ( 5832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.37 seconds wall clock time: 53 minutes 8.40 seconds (3188.40 seconds total)