Starting phenix.real_space_refine on Tue Jan 14 12:26:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0t_39033/01_2025/8z0t_39033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0t_39033/01_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_39033/01_2025/8z0t_39033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0t_39033/01_2025/8z0t_39033.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0t_39033/01_2025/8z0t_39033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0t_39033/01_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-5571/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: 4.27, per 1000 atoms: 0.65 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: 1.73 Conformation dependent library (CDL) restraints added in 955.0 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: 0.97 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: 1.76 Time building geometry restraints manager: 1.98 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: 1.380 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.310 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- 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 : 0.732 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: 0.1669 time to fit residues: 23.5757 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 : 0.778 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9982 ------------------------------------------------------------------------------- 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 D 361 HIS E 399 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107378 restraints weight = 10808.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109426 restraints weight = 6232.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110705 restraints weight = 4956.334| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6717 Z= 0.287 Angle : 0.648 6.565 9155 Z= 0.323 Chirality : 0.047 0.368 1073 Planarity : 0.004 0.038 1157 Dihedral : 10.499 60.334 1220 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.06 % Allowed : 29.09 % Favored : 66.85 % 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: -1.57 (0.74), residues: 35 sheet: -0.02 (0.29), residues: 323 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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: 29 poor density : 96 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7364 (mp10) outliers start: 29 outliers final: 17 residues processed: 121 average time/residue: 0.1598 time to fit residues: 27.4824 Evaluate side-chains 106 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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: 0.9980 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.141416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108765 restraints weight = 10985.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109753 restraints weight = 8129.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110845 restraints weight = 5984.088| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6717 Z= 0.207 Angle : 0.595 5.781 9155 Z= 0.295 Chirality : 0.046 0.355 1073 Planarity : 0.004 0.035 1157 Dihedral : 8.665 54.758 1220 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.45 % Allowed : 28.67 % Favored : 65.87 % 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: -0.77 (0.29), residues: 796 helix: -1.08 (0.80), residues: 35 sheet: -0.08 (0.29), residues: 337 loop : -0.76 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 149 HIS 0.004 0.001 HIS D 371 PHE 0.006 0.001 PHE E 385 TYR 0.007 0.001 TYR A 175 ARG 0.003 0.000 ARG E 308 *********************** 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 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7806 (tppt) cc_final: 0.7563 (tppt) REVERT: A 94 GLN cc_start: 0.8052 (tt0) cc_final: 0.7818 (tt0) REVERT: D 132 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: E 184 HIS cc_start: 0.7946 (m90) cc_final: 0.7637 (m90) REVERT: E 221 LEU cc_start: 0.8429 (tp) cc_final: 0.8090 (tp) outliers start: 39 outliers final: 24 residues processed: 135 average time/residue: 0.1444 time to fit residues: 28.0583 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 : 0.625 ------------------------------------------------------------------------------- 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 160 LEU 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 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: 0.8980 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 25 optimal weight: 0.6980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 133 HIS A 182 GLN D 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107581 restraints weight = 10948.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109344 restraints weight = 8017.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110788 restraints weight = 6056.498| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6717 Z= 0.193 Angle : 0.583 6.120 9155 Z= 0.289 Chirality : 0.046 0.360 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.437 41.805 1218 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.90 % Allowed : 28.67 % 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: -0.66 (0.29), residues: 796 helix: -0.21 (0.83), residues: 34 sheet: -0.02 (0.29), residues: 337 loop : -0.75 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 149 HIS 0.004 0.001 HIS D 371 PHE 0.007 0.001 PHE D 385 TYR 0.010 0.001 TYR A 185 ARG 0.003 0.000 ARG D 312 *********************** 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 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7824 (tppt) cc_final: 0.7581 (tppt) REVERT: D 132 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: D 306 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8234 (mp) REVERT: E 221 LEU cc_start: 0.8444 (tp) cc_final: 0.8076 (tp) outliers start: 35 outliers final: 26 residues processed: 133 average time/residue: 0.1446 time to fit residues: 27.2934 Evaluate side-chains 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 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 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR 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 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: 6.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.0470 chunk 18 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3777 r_free = 0.3777 target = 0.141758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105659 restraints weight = 10938.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108940 restraints weight = 6520.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111037 restraints weight = 4755.630| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6717 Z= 0.198 Angle : 0.578 6.042 9155 Z= 0.287 Chirality : 0.045 0.342 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.056 40.423 1218 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.01 % Allowed : 26.57 % Favored : 67.41 % 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: -0.59 (0.29), residues: 796 helix: 0.01 (0.83), residues: 35 sheet: 0.03 (0.29), residues: 334 loop : -0.72 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 149 HIS 0.003 0.001 HIS D 371 PHE 0.007 0.001 PHE E 387 TYR 0.011 0.001 TYR A 185 ARG 0.002 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 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7854 (tppt) cc_final: 0.7631 (tppt) REVERT: D 132 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: D 154 GLN cc_start: 0.6843 (tm130) cc_final: 0.6295 (tm130) REVERT: D 306 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8248 (mp) REVERT: E 184 HIS cc_start: 0.8074 (m90) cc_final: 0.7791 (m90) REVERT: E 221 LEU cc_start: 0.8497 (tp) cc_final: 0.8104 (tp) outliers start: 43 outliers final: 33 residues processed: 134 average time/residue: 0.1374 time to fit residues: 26.3135 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 : 0.765 ------------------------------------------------------------------------------- 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 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 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 329 PHE 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: 2.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3729 r_free = 0.3729 target = 0.139210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105776 restraints weight = 10571.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106893 restraints weight = 7940.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107944 restraints weight = 5945.950| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6717 Z= 0.256 Angle : 0.594 5.569 9155 Z= 0.297 Chirality : 0.046 0.361 1073 Planarity : 0.004 0.034 1157 Dihedral : 7.013 42.509 1218 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.59 % Allowed : 26.57 % Favored : 67.83 % 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: -0.58 (0.30), residues: 796 helix: 0.35 (0.90), residues: 34 sheet: -0.04 (0.28), residues: 336 loop : -0.68 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 149 HIS 0.003 0.001 HIS D 361 PHE 0.008 0.001 PHE E 387 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 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7879 (tppt) cc_final: 0.7660 (tppt) REVERT: D 132 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: D 154 GLN cc_start: 0.6975 (tm130) cc_final: 0.6400 (tm130) REVERT: D 306 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8348 (mp) outliers start: 40 outliers final: 35 residues processed: 135 average time/residue: 0.1938 time to fit residues: 36.7237 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 158 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 24 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.140294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106464 restraints weight = 10616.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107549 restraints weight = 8220.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108713 restraints weight = 6055.922| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6717 Z= 0.211 Angle : 0.588 6.126 9155 Z= 0.294 Chirality : 0.045 0.341 1073 Planarity : 0.004 0.032 1157 Dihedral : 6.754 40.624 1218 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 6.57 % Allowed : 26.15 % 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: 0.32 (0.89), residues: 34 sheet: -0.01 (0.29), residues: 336 loop : -0.65 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 64 HIS 0.003 0.001 HIS D 361 PHE 0.008 0.001 PHE E 385 TYR 0.012 0.001 TYR A 175 ARG 0.002 0.000 ARG E 232 *********************** 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 144 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7913 (tppt) cc_final: 0.7710 (tppt) REVERT: D 132 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: D 306 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8306 (mp) REVERT: E 184 HIS cc_start: 0.8045 (m90) cc_final: 0.7791 (m90) REVERT: E 221 LEU cc_start: 0.8482 (tp) cc_final: 0.8208 (tp) REVERT: E 289 ARG cc_start: 0.7684 (tpm170) cc_final: 0.6986 (tpm170) outliers start: 47 outliers final: 39 residues processed: 136 average time/residue: 0.1443 time to fit residues: 27.9485 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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 158 VAL 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 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 329 PHE 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 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 = 0.3731 r_free = 0.3731 target = 0.139476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105924 restraints weight = 10671.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107172 restraints weight = 8100.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108294 restraints weight = 6019.763| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6717 Z= 0.235 Angle : 0.590 6.051 9155 Z= 0.295 Chirality : 0.045 0.343 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.698 40.767 1218 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.87 % Allowed : 26.85 % Favored : 67.27 % 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: -0.53 (0.30), residues: 796 helix: 0.27 (0.91), residues: 34 sheet: -0.00 (0.28), residues: 336 loop : -0.62 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.002 0.001 HIS A 95 PHE 0.008 0.001 PHE E 385 TYR 0.014 0.001 TYR A 185 ARG 0.001 0.000 ARG D 341 *********************** 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 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: D 306 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8358 (mp) REVERT: E 184 HIS cc_start: 0.8024 (m90) cc_final: 0.7750 (m90) REVERT: E 221 LEU cc_start: 0.8550 (tp) cc_final: 0.8255 (tp) outliers start: 42 outliers final: 36 residues processed: 133 average time/residue: 0.1571 time to fit residues: 29.5464 Evaluate side-chains 133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 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 158 VAL 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 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: 0.0870 chunk 18 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106903 restraints weight = 10968.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108969 restraints weight = 7893.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110967 restraints weight = 5475.767| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6717 Z= 0.167 Angle : 0.589 6.715 9155 Z= 0.294 Chirality : 0.045 0.330 1073 Planarity : 0.004 0.032 1157 Dihedral : 6.268 38.792 1218 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.31 % Allowed : 27.27 % Favored : 67.41 % 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: -0.45 (0.30), residues: 796 helix: 0.14 (0.89), residues: 34 sheet: 0.08 (0.29), residues: 337 loop : -0.58 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 149 HIS 0.002 0.000 HIS A 95 PHE 0.009 0.001 PHE D 385 TYR 0.014 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 143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: D 306 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8303 (mp) REVERT: E 184 HIS cc_start: 0.7958 (m90) cc_final: 0.7666 (m90) REVERT: E 191 TYR cc_start: 0.7864 (m-80) cc_final: 0.7618 (m-80) REVERT: E 221 LEU cc_start: 0.8383 (tp) cc_final: 0.8137 (tp) outliers start: 38 outliers final: 32 residues processed: 135 average time/residue: 0.1449 time to fit residues: 27.8916 Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 135 CYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 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 329 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.0070 chunk 14 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.141495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107637 restraints weight = 11001.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109149 restraints weight = 7823.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110956 restraints weight = 5728.293| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6717 Z= 0.189 Angle : 0.589 6.919 9155 Z= 0.295 Chirality : 0.045 0.337 1073 Planarity : 0.004 0.032 1157 Dihedral : 6.162 37.850 1217 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.76 % Allowed : 27.83 % Favored : 67.41 % 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: -0.42 (0.30), residues: 796 helix: 0.11 (0.89), residues: 34 sheet: 0.09 (0.29), residues: 336 loop : -0.55 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 149 HIS 0.004 0.001 HIS D 126 PHE 0.009 0.001 PHE E 385 TYR 0.026 0.001 TYR A 185 ARG 0.004 0.000 ARG E 289 ********************** 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 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: D 390 LEU cc_start: 0.8227 (tp) cc_final: 0.8016 (tt) REVERT: E 184 HIS cc_start: 0.7881 (m90) cc_final: 0.7595 (m90) REVERT: E 191 TYR cc_start: 0.7903 (m-80) cc_final: 0.7650 (m-80) REVERT: E 221 LEU cc_start: 0.8494 (tp) cc_final: 0.8234 (tp) REVERT: E 311 MET cc_start: 0.7571 (mtp) cc_final: 0.7349 (mtp) outliers start: 34 outliers final: 31 residues processed: 128 average time/residue: 0.1395 time to fit residues: 25.9269 Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 135 CYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.0000 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107661 restraints weight = 11096.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109121 restraints weight = 8159.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111395 restraints weight = 5639.145| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6717 Z= 0.188 Angle : 0.595 8.571 9155 Z= 0.296 Chirality : 0.045 0.331 1073 Planarity : 0.004 0.032 1157 Dihedral : 6.061 37.597 1217 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.76 % Allowed : 28.11 % Favored : 67.13 % 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: -0.41 (0.30), residues: 796 helix: 0.02 (0.88), residues: 34 sheet: 0.11 (0.29), residues: 336 loop : -0.54 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 149 HIS 0.006 0.001 HIS D 126 PHE 0.008 0.001 PHE E 385 TYR 0.023 0.001 TYR A 185 ARG 0.007 0.000 ARG E 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.60 seconds wall clock time: 41 minutes 46.12 seconds (2506.12 seconds total)