Starting phenix.real_space_refine on Wed Sep 17 07:21:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0t_39033/09_2025/8z0t_39033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0t_39033/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z0t_39033/09_2025/8z0t_39033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0t_39033/09_2025/8z0t_39033.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z0t_39033/09_2025/8z0t_39033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0t_39033/09_2025/8z0t_39033.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.50, per 1000 atoms: 0.23 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: 0.57 Conformation dependent library (CDL) restraints added in 318.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.18 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: 1.03 Time building geometry restraints manager: 0.72 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: 1.570 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.500 ------------------------------------------------------------------------------- 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 6744 Z= 0.259 Angle : 1.022 13.878 9226 Z= 0.509 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 : 6.06 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG E 289 TYR 0.044 0.002 TYR A 185 PHE 0.040 0.003 PHE A 56 TRP 0.053 0.002 TRP D 149 HIS 0.011 0.001 HIS D 361 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 6717) covalent geometry : angle 0.98102 ( 9155) SS BOND : bond 0.00188 ( 10) SS BOND : angle 1.22473 ( 20) hydrogen bonds : bond 0.14536 ( 222) hydrogen bonds : angle 6.67878 ( 624) link_BETA1-4 : bond 0.00619 ( 8) link_BETA1-4 : angle 2.65920 ( 24) link_NAG-ASN : bond 0.01383 ( 9) link_NAG-ASN : angle 4.79273 ( 27) *********************** 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 : 0.249 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: 0.0722 time to fit residues: 10.2934 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 : 0.309 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0670 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0470 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108457 restraints weight = 10880.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111780 restraints weight = 6384.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113945 restraints weight = 4622.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115289 restraints weight = 3782.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115830 restraints weight = 3358.067| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6744 Z= 0.121 Angle : 0.643 7.453 9226 Z= 0.312 Chirality : 0.045 0.347 1073 Planarity : 0.004 0.038 1157 Dihedral : 10.454 61.882 1220 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.92 % Allowed : 28.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.29), residues: 796 helix: -1.71 (0.73), residues: 35 sheet: -0.08 (0.29), residues: 336 loop : -0.91 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 341 TYR 0.013 0.001 TYR A 185 PHE 0.005 0.001 PHE E 350 TRP 0.012 0.001 TRP D 149 HIS 0.003 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6717) covalent geometry : angle 0.61348 ( 9155) SS BOND : bond 0.00572 ( 10) SS BOND : angle 0.88426 ( 20) hydrogen bonds : bond 0.03228 ( 222) hydrogen bonds : angle 5.17711 ( 624) link_BETA1-4 : bond 0.00490 ( 8) link_BETA1-4 : angle 2.15207 ( 24) link_NAG-ASN : bond 0.00794 ( 9) link_NAG-ASN : angle 2.96795 ( 27) *********************** 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 133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7817 (tppt) cc_final: 0.7584 (mmtt) REVERT: D 132 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: D 241 VAL cc_start: 0.9240 (t) cc_final: 0.8975 (t) outliers start: 28 outliers final: 16 residues processed: 130 average time/residue: 0.0684 time to fit residues: 12.5889 Evaluate side-chains 112 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 152 LEU 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 329 PHE 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 283 THR 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 73 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 E 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107835 restraints weight = 10819.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109244 restraints weight = 6224.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109787 restraints weight = 4982.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110560 restraints weight = 4585.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110717 restraints weight = 4343.271| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6744 Z= 0.151 Angle : 0.636 7.244 9226 Z= 0.307 Chirality : 0.046 0.359 1073 Planarity : 0.004 0.035 1157 Dihedral : 8.730 48.959 1218 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.31 % Allowed : 28.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.29), residues: 796 helix: -1.21 (0.79), residues: 35 sheet: -0.06 (0.29), residues: 336 loop : -0.77 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 308 TYR 0.012 0.001 TYR A 185 PHE 0.006 0.001 PHE E 329 TRP 0.022 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6717) covalent geometry : angle 0.60564 ( 9155) SS BOND : bond 0.00465 ( 10) SS BOND : angle 0.92640 ( 20) hydrogen bonds : bond 0.03133 ( 222) hydrogen bonds : angle 4.99250 ( 624) link_BETA1-4 : bond 0.00442 ( 8) link_BETA1-4 : angle 2.25130 ( 24) link_NAG-ASN : bond 0.00776 ( 9) link_NAG-ASN : angle 2.97789 ( 27) *********************** 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 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7784 (tppt) cc_final: 0.7501 (tppt) REVERT: A 94 GLN cc_start: 0.8099 (tt0) cc_final: 0.7848 (tt0) REVERT: D 132 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: E 184 HIS cc_start: 0.8011 (m90) cc_final: 0.7714 (m90) outliers start: 38 outliers final: 23 residues processed: 129 average time/residue: 0.0606 time to fit residues: 11.3977 Evaluate side-chains 116 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 164 THR 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 317 THR Chi-restraints excluded: chain D residue 331 THR 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 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 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 39 optimal weight: 0.2980 chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105564 restraints weight = 10864.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108801 restraints weight = 6444.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110858 restraints weight = 4705.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111985 restraints weight = 3891.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112874 restraints weight = 3489.700| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6744 Z= 0.130 Angle : 0.613 6.889 9226 Z= 0.296 Chirality : 0.045 0.343 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.659 40.627 1218 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.29), residues: 796 helix: -0.48 (0.79), residues: 34 sheet: -0.02 (0.29), residues: 336 loop : -0.77 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 341 TYR 0.009 0.001 TYR A 185 PHE 0.008 0.001 PHE E 403 TRP 0.013 0.001 TRP D 149 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6717) covalent geometry : angle 0.58391 ( 9155) SS BOND : bond 0.00213 ( 10) SS BOND : angle 0.79760 ( 20) hydrogen bonds : bond 0.02879 ( 222) hydrogen bonds : angle 4.79237 ( 624) link_BETA1-4 : bond 0.00462 ( 8) link_BETA1-4 : angle 2.18317 ( 24) link_NAG-ASN : bond 0.00739 ( 9) link_NAG-ASN : angle 2.87249 ( 27) *********************** 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 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7748 (tppt) cc_final: 0.7505 (tppt) REVERT: D 132 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: D 154 GLN cc_start: 0.6876 (tm130) cc_final: 0.6313 (tm130) REVERT: D 306 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8206 (mp) outliers start: 34 outliers final: 27 residues processed: 129 average time/residue: 0.0610 time to fit residues: 11.5460 Evaluate side-chains 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 164 THR 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 306 LEU 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 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 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 34 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101989 restraints weight = 11006.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102983 restraints weight = 8401.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104708 restraints weight = 5879.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104932 restraints weight = 5085.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105408 restraints weight = 4616.452| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 6744 Z= 0.258 Angle : 0.704 9.065 9226 Z= 0.343 Chirality : 0.048 0.363 1073 Planarity : 0.004 0.037 1157 Dihedral : 8.207 48.827 1218 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.57 % Allowed : 26.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.29), residues: 796 helix: -0.35 (0.89), residues: 36 sheet: -0.01 (0.29), residues: 318 loop : -0.76 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 341 TYR 0.011 0.002 TYR D 297 PHE 0.013 0.002 PHE E 387 TRP 0.025 0.002 TRP D 149 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 6717) covalent geometry : angle 0.67201 ( 9155) SS BOND : bond 0.00433 ( 10) SS BOND : angle 0.89136 ( 20) hydrogen bonds : bond 0.03240 ( 222) hydrogen bonds : angle 5.07802 ( 624) link_BETA1-4 : bond 0.00355 ( 8) link_BETA1-4 : angle 2.49372 ( 24) link_NAG-ASN : bond 0.00771 ( 9) link_NAG-ASN : angle 3.16467 ( 27) *********************** 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 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7832 (tppt) cc_final: 0.7630 (tppt) REVERT: D 132 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: D 243 ASP cc_start: 0.8068 (m-30) cc_final: 0.7827 (m-30) REVERT: D 306 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8571 (mp) REVERT: E 184 HIS cc_start: 0.8112 (m90) cc_final: 0.7827 (m90) outliers start: 47 outliers final: 34 residues processed: 129 average time/residue: 0.0641 time to fit residues: 11.7711 Evaluate side-chains 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 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 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 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 25 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.138157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104107 restraints weight = 10768.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105175 restraints weight = 8490.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106237 restraints weight = 6216.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106879 restraints weight = 5243.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107316 restraints weight = 4897.554| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6744 Z= 0.155 Angle : 0.641 7.538 9226 Z= 0.311 Chirality : 0.046 0.349 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.474 42.486 1218 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.73 % Allowed : 26.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.29), residues: 796 helix: 0.25 (0.90), residues: 35 sheet: -0.15 (0.28), residues: 333 loop : -0.77 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 289 TYR 0.007 0.001 TYR A 174 PHE 0.008 0.001 PHE D 385 TRP 0.015 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6717) covalent geometry : angle 0.61209 ( 9155) SS BOND : bond 0.00222 ( 10) SS BOND : angle 0.84705 ( 20) hydrogen bonds : bond 0.02862 ( 222) hydrogen bonds : angle 4.90211 ( 624) link_BETA1-4 : bond 0.00420 ( 8) link_BETA1-4 : angle 2.16522 ( 24) link_NAG-ASN : bond 0.00719 ( 9) link_NAG-ASN : angle 2.97289 ( 27) *********************** 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 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7490 (mp10) REVERT: D 243 ASP cc_start: 0.7997 (m-30) cc_final: 0.7774 (m-30) REVERT: D 306 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8564 (mp) outliers start: 41 outliers final: 29 residues processed: 131 average time/residue: 0.0686 time to fit residues: 12.7332 Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 292 ILE 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 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 243 ASP 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 71 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.138747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102863 restraints weight = 10806.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106023 restraints weight = 6508.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108086 restraints weight = 4796.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109341 restraints weight = 3975.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109989 restraints weight = 3543.488| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6744 Z= 0.157 Angle : 0.639 7.328 9226 Z= 0.310 Chirality : 0.046 0.349 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.193 41.696 1218 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.29), residues: 796 helix: 0.27 (0.91), residues: 34 sheet: -0.10 (0.28), residues: 333 loop : -0.73 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 341 TYR 0.013 0.001 TYR A 185 PHE 0.008 0.001 PHE D 385 TRP 0.030 0.002 TRP A 64 HIS 0.003 0.001 HIS E 361 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6717) covalent geometry : angle 0.60994 ( 9155) SS BOND : bond 0.00209 ( 10) SS BOND : angle 0.77528 ( 20) hydrogen bonds : bond 0.02800 ( 222) hydrogen bonds : angle 4.86944 ( 624) link_BETA1-4 : bond 0.00430 ( 8) link_BETA1-4 : angle 2.20315 ( 24) link_NAG-ASN : bond 0.00710 ( 9) link_NAG-ASN : angle 2.91945 ( 27) *********************** 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 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7952 (tt0) cc_final: 0.7721 (tt0) REVERT: D 132 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: D 243 ASP cc_start: 0.8011 (m-30) cc_final: 0.7742 (m-30) REVERT: D 306 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8574 (mp) REVERT: E 184 HIS cc_start: 0.8043 (m90) cc_final: 0.7798 (m90) outliers start: 38 outliers final: 33 residues processed: 132 average time/residue: 0.0643 time to fit residues: 12.2319 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 209 CYS Chi-restraints excluded: chain D residue 241 VAL 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 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER 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 11 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.139853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105157 restraints weight = 10977.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106304 restraints weight = 8112.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107737 restraints weight = 6015.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108107 restraints weight = 5225.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108502 restraints weight = 4709.321| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6744 Z= 0.126 Angle : 0.623 6.750 9226 Z= 0.302 Chirality : 0.045 0.341 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.768 39.623 1218 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.90 % Allowed : 27.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.30), residues: 796 helix: 0.27 (0.90), residues: 34 sheet: -0.05 (0.28), residues: 332 loop : -0.68 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 232 TYR 0.014 0.001 TYR A 185 PHE 0.009 0.001 PHE D 385 TRP 0.017 0.001 TRP A 64 HIS 0.003 0.001 HIS E 361 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6717) covalent geometry : angle 0.59553 ( 9155) SS BOND : bond 0.00152 ( 10) SS BOND : angle 0.71310 ( 20) hydrogen bonds : bond 0.02698 ( 222) hydrogen bonds : angle 4.76293 ( 624) link_BETA1-4 : bond 0.00441 ( 8) link_BETA1-4 : angle 2.09487 ( 24) link_NAG-ASN : bond 0.00696 ( 9) link_NAG-ASN : angle 2.82651 ( 27) *********************** 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 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: D 243 ASP cc_start: 0.8045 (m-30) cc_final: 0.7828 (m-30) REVERT: E 184 HIS cc_start: 0.8265 (m90) cc_final: 0.7982 (m90) outliers start: 35 outliers final: 31 residues processed: 128 average time/residue: 0.0615 time to fit residues: 11.4326 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 209 CYS Chi-restraints excluded: chain D residue 241 VAL 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 243 ASP Chi-restraints excluded: chain E residue 256 SER 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 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.0020 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104040 restraints weight = 10959.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107325 restraints weight = 6540.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109396 restraints weight = 4780.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110685 restraints weight = 3952.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111352 restraints weight = 3522.693| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6744 Z= 0.129 Angle : 0.626 7.171 9226 Z= 0.304 Chirality : 0.045 0.340 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.482 39.097 1218 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.17 % Allowed : 27.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.30), residues: 796 helix: 0.24 (0.89), residues: 34 sheet: 0.04 (0.28), residues: 337 loop : -0.67 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 232 TYR 0.013 0.001 TYR A 185 PHE 0.009 0.001 PHE D 385 TRP 0.019 0.001 TRP D 149 HIS 0.003 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6717) covalent geometry : angle 0.59923 ( 9155) SS BOND : bond 0.00172 ( 10) SS BOND : angle 0.80241 ( 20) hydrogen bonds : bond 0.02721 ( 222) hydrogen bonds : angle 4.71242 ( 624) link_BETA1-4 : bond 0.00401 ( 8) link_BETA1-4 : angle 2.12893 ( 24) link_NAG-ASN : bond 0.00679 ( 9) link_NAG-ASN : angle 2.79372 ( 27) *********************** 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 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8078 (tt0) cc_final: 0.7835 (tt0) REVERT: D 132 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: E 184 HIS cc_start: 0.8183 (m90) cc_final: 0.7886 (m90) outliers start: 37 outliers final: 34 residues processed: 134 average time/residue: 0.0594 time to fit residues: 11.5158 Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 292 ILE 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 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER 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 5 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 chunk 53 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.104661 restraints weight = 10833.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107858 restraints weight = 6423.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109972 restraints weight = 4673.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111236 restraints weight = 3835.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111928 restraints weight = 3411.920| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6744 Z= 0.127 Angle : 0.615 6.849 9226 Z= 0.299 Chirality : 0.045 0.337 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.332 38.489 1218 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.90 % Allowed : 27.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.30), residues: 796 helix: 0.19 (0.89), residues: 34 sheet: 0.10 (0.29), residues: 337 loop : -0.64 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 289 TYR 0.017 0.001 TYR A 185 PHE 0.009 0.001 PHE E 385 TRP 0.019 0.001 TRP D 149 HIS 0.003 0.001 HIS E 409 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6717) covalent geometry : angle 0.58769 ( 9155) SS BOND : bond 0.00164 ( 10) SS BOND : angle 0.80359 ( 20) hydrogen bonds : bond 0.02647 ( 222) hydrogen bonds : angle 4.65668 ( 624) link_BETA1-4 : bond 0.00408 ( 8) link_BETA1-4 : angle 2.07427 ( 24) link_NAG-ASN : bond 0.00673 ( 9) link_NAG-ASN : angle 2.76139 ( 27) ********************** 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 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: E 184 HIS cc_start: 0.8169 (m90) cc_final: 0.7865 (m90) outliers start: 35 outliers final: 33 residues processed: 128 average time/residue: 0.0609 time to fit residues: 11.3731 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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 292 ILE 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 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS 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 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103468 restraints weight = 10849.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106611 restraints weight = 6447.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108644 restraints weight = 4702.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109921 restraints weight = 3890.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110694 restraints weight = 3455.525| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6744 Z= 0.150 Angle : 0.634 7.212 9226 Z= 0.306 Chirality : 0.045 0.340 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.414 39.468 1218 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.31 % Allowed : 27.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.30), residues: 796 helix: 0.23 (0.90), residues: 34 sheet: 0.08 (0.29), residues: 337 loop : -0.63 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 289 TYR 0.027 0.001 TYR A 185 PHE 0.008 0.001 PHE E 385 TRP 0.018 0.001 TRP D 149 HIS 0.003 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6717) covalent geometry : angle 0.60679 ( 9155) SS BOND : bond 0.00194 ( 10) SS BOND : angle 0.79761 ( 20) hydrogen bonds : bond 0.02722 ( 222) hydrogen bonds : angle 4.71072 ( 624) link_BETA1-4 : bond 0.00351 ( 8) link_BETA1-4 : angle 2.14529 ( 24) link_NAG-ASN : bond 0.00669 ( 9) link_NAG-ASN : angle 2.79751 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.64 seconds wall clock time: 22 minutes 24.30 seconds (1344.30 seconds total)