Starting phenix.real_space_refine on Tue Mar 11 20:13:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0t_39033/03_2025/8z0t_39033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0t_39033/03_2025/8z0t_39033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0t_39033/03_2025/8z0t_39033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0t_39033/03_2025/8z0t_39033.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0t_39033/03_2025/8z0t_39033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0t_39033/03_2025/8z0t_39033.cif" } resolution = 3.58 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= -0.000 sd= 0.026 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 27 5.16 5 C 4096 2.51 5 N 1121 2.21 5 O 1312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6556 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1393 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 162} Chain: "D" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2467 Classifications: {'peptide': 316} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2467 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 292} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} 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 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.96, per 1000 atoms: 0.76 Number of scatterers: 6556 At special positions: 0 Unit cell: (101.65, 87.74, 116.63, 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 27 16.00 O 1312 8.00 N 1121 7.00 C 4096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 209 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS D 239 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 405 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 405 " distance=2.03 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 B 2 " - " BMA B 3 " " BMA B 3 " - " NAG B 4 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 301 " - " ASN A 46 " " NAG A 302 " - " ASN A 191 " " NAG A 303 " - " ASN A 99 " " NAG A 304 " - " ASN A 165 " " NAG B 1 " - " ASN A 67 " " NAG C 1 " - " ASN A 160 " " NAG E 501 " - " ASN E 252 " " NAG F 1 " - " ASN D 275 " " NAG G 1 " - " ASN E 275 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 918.8 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 20 sheets defined 6.7% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.601A pdb=" N ASP A 87 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'D' and resid 181 through 187 removed outlier: 3.523A pdb=" N TRP D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.742A pdb=" N ASP E 188 " --> pdb=" O TRP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 294 Processing helix chain 'E' and resid 393 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.641A pdb=" N VAL A 47 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.256A pdb=" N ILE A 41 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP A 64 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 117 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.841A pdb=" N LYS A 179 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 142 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 143 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 154 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR A 145 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 150 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'D' and resid 113 through 117 removed outlier: 6.023A pdb=" N ALA D 172 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.880A pdb=" N ASN D 146 " --> pdb=" O THR D 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 222 removed outlier: 3.786A pdb=" N THR D 238 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP D 243 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 278 " --> pdb=" O ASP D 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 252 through 257 Processing sheet with id=AB1, first strand: chain 'D' and resid 325 through 329 removed outlier: 5.865A pdb=" N PHE D 384 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 356 through 360 Processing sheet with id=AB3, first strand: chain 'E' and resid 113 through 118 removed outlier: 5.842A pdb=" N ALA E 172 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 113 through 118 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.580A pdb=" N ASP E 204 " --> pdb=" O CYS E 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.908A pdb=" N THR E 238 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.908A pdb=" N THR E 238 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 252 through 256 Processing sheet with id=AB9, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AC1, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AC2, first strand: chain 'E' and resid 364 through 365 removed outlier: 3.612A pdb=" N CYS E 405 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 418 " --> pdb=" O ALA E 407 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 624 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: 2.17 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2019 1.34 - 1.46: 1572 1.46 - 1.58: 3091 1.58 - 1.70: 1 1.70 - 1.82: 34 Bond restraints: 6717 Sorted by residual: bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " ideal model delta sigma weight residual 1.528 1.575 -0.047 2.00e-02 2.50e+03 5.44e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.96e+00 bond pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " ideal model delta sigma weight residual 1.541 1.585 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 6712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 8946 2.78 - 5.55: 169 5.55 - 8.33: 31 8.33 - 11.10: 7 11.10 - 13.88: 2 Bond angle restraints: 9155 Sorted by residual: angle pdb=" C ASP E 122 " pdb=" N GLY E 123 " pdb=" CA GLY E 123 " ideal model delta sigma weight residual 121.70 135.58 -13.88 1.80e+00 3.09e-01 5.94e+01 angle pdb=" C HIS E 361 " pdb=" N ASN E 362 " pdb=" CA ASN E 362 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C PHE E 227 " pdb=" N ASP E 228 " pdb=" CA ASP E 228 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" CA VAL E 242 " pdb=" CB VAL E 242 " pdb=" CG1 VAL E 242 " ideal model delta sigma weight residual 110.40 118.15 -7.75 1.70e+00 3.46e-01 2.08e+01 angle pdb=" CB MET E 351 " pdb=" CG MET E 351 " pdb=" SD MET E 351 " ideal model delta sigma weight residual 112.70 125.96 -13.26 3.00e+00 1.11e-01 1.95e+01 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 3744 21.71 - 43.41: 414 43.41 - 65.12: 67 65.12 - 86.83: 31 86.83 - 108.54: 10 Dihedral angle restraints: 4266 sinusoidal: 1931 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual 93.00 28.70 64.30 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CA VAL E 242 " pdb=" C VAL E 242 " pdb=" N ASP E 243 " pdb=" CA ASP E 243 " ideal model delta harmonic sigma weight residual 180.00 143.82 36.18 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CB CYS D 121 " pdb=" SG CYS D 121 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual 93.00 146.37 -53.37 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 4263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1037 0.133 - 0.266: 30 0.266 - 0.398: 4 0.398 - 0.531: 1 0.531 - 0.664: 1 Chirality restraints: 1073 Sorted by residual: chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C1 NAG A 303 " pdb=" ND2 ASN A 99 " pdb=" C2 NAG A 303 " pdb=" O5 NAG A 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CB ILE E 116 " pdb=" CA ILE E 116 " pdb=" CG1 ILE E 116 " pdb=" CG2 ILE E 116 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 1070 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 242 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C VAL E 242 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL E 242 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP E 243 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 149 " 0.021 2.00e-02 2.50e+03 1.95e-02 9.53e+00 pdb=" CG TRP D 149 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP D 149 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 149 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 149 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 149 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 149 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 149 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 149 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " -0.012 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR A 185 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " 0.000 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1395 2.79 - 3.32: 5429 3.32 - 3.84: 11037 3.84 - 4.37: 11823 4.37 - 4.90: 21302 Nonbonded interactions: 50986 Sorted by model distance: nonbonded pdb=" O LYS D 183 " pdb=" OG SER D 187 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 170 " pdb=" OH TYR A 174 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR E 393 " pdb=" OE1 GLU E 396 " model vdw 2.301 3.040 nonbonded pdb=" O THR D 196 " pdb=" OG1 THR D 196 " model vdw 2.318 3.040 nonbonded pdb=" OG SER A 33 " pdb=" OG1 THR A 50 " model vdw 2.348 3.040 ... (remaining 50981 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 'D' selection = (chain 'E' and resid 110 through 425) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.880 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.210 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.005 0.057 6717 Z= 0.359 Angle : 0.981 13.878 9155 Z= 0.501 Chirality : 0.062 0.664 1073 Planarity : 0.007 0.057 1157 Dihedral : 19.033 108.536 2722 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.98 % Allowed : 31.47 % Favored : 67.55 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.28), residues: 796 helix: -3.15 (0.51), residues: 35 sheet: -0.04 (0.29), residues: 318 loop : -1.25 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 149 HIS 0.011 0.001 HIS D 361 PHE 0.040 0.003 PHE A 56 TYR 0.044 0.002 TYR A 185 ARG 0.007 0.000 ARG E 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7847 (tppt) cc_final: 0.7600 (mmtt) outliers start: 7 outliers final: 3 residues processed: 102 average time/residue: 0.1631 time to fit residues: 23.1835 Evaluate side-chains 93 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 209 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN D 154 GLN E 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107344 restraints weight = 10808.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109510 restraints weight = 6239.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110731 restraints weight = 4952.346| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6717 Z= 0.291 Angle : 0.648 6.508 9155 Z= 0.324 Chirality : 0.047 0.367 1073 Planarity : 0.004 0.039 1157 Dihedral : 10.604 61.492 1220 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.20 % Allowed : 28.81 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % 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 (0.29), residues: 796 helix: -1.59 (0.74), residues: 35 sheet: -0.02 (0.29), residues: 323 loop : -0.88 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 PHE 0.008 0.001 PHE E 350 TYR 0.014 0.001 TYR A 185 ARG 0.003 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7369 (mp10) outliers start: 30 outliers final: 17 residues processed: 121 average time/residue: 0.1508 time to fit residues: 25.6948 Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN D 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108095 restraints weight = 10981.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110450 restraints weight = 6241.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112500 restraints weight = 4907.808| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6717 Z= 0.208 Angle : 0.595 5.636 9155 Z= 0.296 Chirality : 0.046 0.356 1073 Planarity : 0.004 0.035 1157 Dihedral : 9.044 54.985 1220 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.31 % Allowed : 28.67 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % 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 (0.29), residues: 796 helix: -1.14 (0.80), residues: 35 sheet: -0.11 (0.29), residues: 337 loop : -0.78 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 149 HIS 0.004 0.001 HIS D 371 PHE 0.006 0.001 PHE D 385 TYR 0.008 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7799 (tppt) cc_final: 0.7545 (tppt) REVERT: D 132 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: E 184 HIS cc_start: 0.7946 (m90) cc_final: 0.7658 (m90) REVERT: E 221 LEU cc_start: 0.8505 (tp) cc_final: 0.8210 (tp) outliers start: 38 outliers final: 24 residues processed: 134 average time/residue: 0.1386 time to fit residues: 26.6465 Evaluate side-chains 117 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106286 restraints weight = 10967.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107265 restraints weight = 8265.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108847 restraints weight = 6352.992| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6717 Z= 0.266 Angle : 0.611 6.246 9155 Z= 0.303 Chirality : 0.047 0.367 1073 Planarity : 0.004 0.034 1157 Dihedral : 7.989 46.383 1218 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.73 % Allowed : 28.11 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % 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: -0.75 (0.30), residues: 796 helix: -0.83 (0.82), residues: 36 sheet: -0.11 (0.29), residues: 334 loop : -0.72 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 PHE 0.007 0.001 PHE E 387 TYR 0.009 0.001 TYR A 185 ARG 0.003 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7847 (tppt) cc_final: 0.7613 (tppt) REVERT: D 132 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: D 306 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8322 (mp) REVERT: D 390 LEU cc_start: 0.8250 (tt) cc_final: 0.7915 (tt) REVERT: E 221 LEU cc_start: 0.8543 (tp) cc_final: 0.8176 (tp) outliers start: 41 outliers final: 34 residues processed: 132 average time/residue: 0.1490 time to fit residues: 27.9069 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104079 restraints weight = 10696.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105038 restraints weight = 8616.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106468 restraints weight = 6175.949| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6717 Z= 0.278 Angle : 0.601 5.845 9155 Z= 0.300 Chirality : 0.046 0.356 1073 Planarity : 0.004 0.034 1157 Dihedral : 7.565 46.419 1218 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 6.85 % Allowed : 26.71 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % 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: -0.71 (0.29), residues: 796 helix: -0.02 (0.85), residues: 35 sheet: -0.06 (0.29), residues: 331 loop : -0.79 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 149 HIS 0.003 0.001 HIS D 361 PHE 0.007 0.001 PHE E 385 TYR 0.010 0.001 TYR A 185 ARG 0.003 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7889 (tppt) cc_final: 0.7657 (tppt) REVERT: D 132 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: E 184 HIS cc_start: 0.8143 (m90) cc_final: 0.7852 (m90) REVERT: E 289 ARG cc_start: 0.7721 (tpm170) cc_final: 0.7090 (tpm170) outliers start: 49 outliers final: 37 residues processed: 132 average time/residue: 0.1450 time to fit residues: 27.0584 Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.138511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104472 restraints weight = 10588.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105102 restraints weight = 8752.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106349 restraints weight = 6381.804| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6717 Z= 0.244 Angle : 0.600 6.134 9155 Z= 0.299 Chirality : 0.046 0.351 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.284 44.551 1218 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 6.15 % Allowed : 26.29 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.67 (0.29), residues: 796 helix: -0.02 (0.87), residues: 35 sheet: -0.03 (0.29), residues: 331 loop : -0.76 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 149 HIS 0.002 0.001 HIS D 409 PHE 0.008 0.001 PHE D 385 TYR 0.010 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7908 (tppt) cc_final: 0.7694 (tppt) REVERT: D 132 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: E 221 LEU cc_start: 0.8513 (tp) cc_final: 0.8214 (tp) outliers start: 44 outliers final: 34 residues processed: 138 average time/residue: 0.1522 time to fit residues: 29.6093 Evaluate side-chains 128 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101408 restraints weight = 10759.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104565 restraints weight = 6402.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106572 restraints weight = 4682.418| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 6717 Z= 0.321 Angle : 0.630 6.764 9155 Z= 0.314 Chirality : 0.047 0.349 1073 Planarity : 0.004 0.034 1157 Dihedral : 7.390 44.058 1218 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.57 % Allowed : 26.29 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.67 (0.30), residues: 796 helix: 0.34 (0.93), residues: 34 sheet: -0.10 (0.28), residues: 333 loop : -0.73 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 64 HIS 0.005 0.001 HIS D 361 PHE 0.007 0.001 PHE E 385 TYR 0.009 0.002 TYR A 175 ARG 0.003 0.000 ARG E 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: E 184 HIS cc_start: 0.8160 (m90) cc_final: 0.7909 (m90) outliers start: 47 outliers final: 37 residues processed: 134 average time/residue: 0.1555 time to fit residues: 29.2381 Evaluate side-chains 131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102427 restraints weight = 10770.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105583 restraints weight = 6413.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107581 restraints weight = 4692.352| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6717 Z= 0.255 Angle : 0.616 6.988 9155 Z= 0.306 Chirality : 0.046 0.333 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.089 41.203 1218 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.45 % Allowed : 27.27 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.59 (0.30), residues: 796 helix: 0.43 (0.94), residues: 34 sheet: -0.05 (0.29), residues: 333 loop : -0.68 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 149 HIS 0.003 0.001 HIS E 361 PHE 0.008 0.001 PHE D 385 TYR 0.014 0.001 TYR A 185 ARG 0.002 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8495 (mp10) cc_final: 0.8291 (mp10) REVERT: D 132 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: E 184 HIS cc_start: 0.8086 (m90) cc_final: 0.7794 (m90) outliers start: 39 outliers final: 35 residues processed: 127 average time/residue: 0.1526 time to fit residues: 27.3029 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102441 restraints weight = 10843.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105633 restraints weight = 6462.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107672 restraints weight = 4706.193| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6717 Z= 0.252 Angle : 0.614 7.434 9155 Z= 0.305 Chirality : 0.046 0.333 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.919 40.894 1218 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.31 % Allowed : 27.41 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.55 (0.30), residues: 796 helix: 0.44 (0.94), residues: 34 sheet: 0.01 (0.29), residues: 338 loop : -0.69 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 149 HIS 0.002 0.001 HIS D 409 PHE 0.008 0.001 PHE D 385 TYR 0.016 0.001 TYR A 185 ARG 0.002 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8144 (tt0) cc_final: 0.7775 (tm-30) REVERT: D 132 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: E 184 HIS cc_start: 0.8084 (m90) cc_final: 0.7787 (m90) REVERT: E 391 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7034 (mt-10) outliers start: 38 outliers final: 36 residues processed: 129 average time/residue: 0.1686 time to fit residues: 30.5780 Evaluate side-chains 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101458 restraints weight = 10936.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104607 restraints weight = 6503.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106516 restraints weight = 4739.339| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 6717 Z= 0.307 Angle : 0.634 7.513 9155 Z= 0.315 Chirality : 0.046 0.335 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.033 41.357 1218 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.73 % Allowed : 27.41 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.56 (0.30), residues: 796 helix: 0.50 (0.96), residues: 34 sheet: -0.02 (0.29), residues: 338 loop : -0.68 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 149 HIS 0.002 0.001 HIS D 409 PHE 0.007 0.001 PHE E 385 TYR 0.017 0.002 TYR A 185 ARG 0.003 0.000 ARG E 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: E 149 TRP cc_start: 0.7319 (m100) cc_final: 0.6377 (m100) REVERT: E 184 HIS cc_start: 0.8093 (m90) cc_final: 0.7788 (m90) REVERT: E 391 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7015 (mt-10) outliers start: 41 outliers final: 35 residues processed: 125 average time/residue: 0.1735 time to fit residues: 30.2883 Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102285 restraints weight = 11036.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105475 restraints weight = 6530.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107507 restraints weight = 4743.098| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6717 Z= 0.253 Angle : 0.629 7.577 9155 Z= 0.313 Chirality : 0.047 0.453 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.852 40.611 1216 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 5.45 % Allowed : 27.55 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.54 (0.30), residues: 796 helix: 0.43 (0.95), residues: 34 sheet: -0.05 (0.29), residues: 333 loop : -0.61 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 149 HIS 0.002 0.001 HIS D 409 PHE 0.008 0.001 PHE D 385 TYR 0.031 0.002 TYR A 185 ARG 0.004 0.000 ARG E 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.69 seconds wall clock time: 40 minutes 32.56 seconds (2432.56 seconds total)