Starting phenix.real_space_refine on Sat May 10 17:07:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0t_39033/05_2025/8z0t_39033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0t_39033/05_2025/8z0t_39033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0t_39033/05_2025/8z0t_39033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0t_39033/05_2025/8z0t_39033.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0t_39033/05_2025/8z0t_39033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0t_39033/05_2025/8z0t_39033.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4096 2.51 5 N 1121 2.21 5 O 1312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6556 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1393 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 162} Chain: "D" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2467 Classifications: {'peptide': 316} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2467 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 292} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.50, per 1000 atoms: 0.69 Number of scatterers: 6556 At special positions: 0 Unit cell: (101.65, 87.74, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1312 8.00 N 1121 7.00 C 4096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 209 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS D 239 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 405 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 405 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " BMA B 3 " - " NAG B 4 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 301 " - " ASN A 46 " " NAG A 302 " - " ASN A 191 " " NAG A 303 " - " ASN A 99 " " NAG A 304 " - " ASN A 165 " " NAG B 1 " - " ASN A 67 " " NAG C 1 " - " ASN A 160 " " NAG E 501 " - " ASN E 252 " " NAG F 1 " - " ASN D 275 " " NAG G 1 " - " ASN E 275 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 901.4 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 20 sheets defined 6.7% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 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: 1.97 Time building geometry restraints manager: 2.09 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.250 Find NCS groups from input model: 0.200 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- 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 : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.98 % Allowed : 31.47 % Favored : 67.55 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.28), residues: 796 helix: -3.15 (0.51), residues: 35 sheet: -0.04 (0.29), residues: 318 loop : -1.25 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 149 HIS 0.011 0.001 HIS D 361 PHE 0.040 0.003 PHE A 56 TYR 0.044 0.002 TYR A 185 ARG 0.007 0.000 ARG E 289 Details of bonding type rmsd link_NAG-ASN : bond 0.01383 ( 9) link_NAG-ASN : angle 4.79273 ( 27) link_BETA1-4 : bond 0.00619 ( 8) link_BETA1-4 : angle 2.65920 ( 24) hydrogen bonds : bond 0.14536 ( 222) hydrogen bonds : angle 6.67878 ( 624) SS BOND : bond 0.00188 ( 10) SS BOND : angle 1.22473 ( 20) covalent geometry : bond 0.00540 ( 6717) covalent geometry : angle 0.98102 ( 9155) *********************** 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 : 0.740 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: 0.1591 time to fit residues: 22.5223 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 : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 209 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN D 154 GLN E 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107342 restraints weight = 10808.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109510 restraints weight = 6240.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110721 restraints weight = 4952.489| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6744 Z= 0.190 Angle : 0.680 7.685 9226 Z= 0.331 Chirality : 0.047 0.367 1073 Planarity : 0.004 0.039 1157 Dihedral : 10.604 61.492 1220 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.20 % Allowed : 28.81 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.29), residues: 796 helix: -1.59 (0.74), residues: 35 sheet: -0.02 (0.29), residues: 323 loop : -0.88 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 149 HIS 0.004 0.001 HIS D 361 PHE 0.008 0.001 PHE E 350 TYR 0.014 0.001 TYR A 185 ARG 0.003 0.000 ARG D 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00846 ( 9) link_NAG-ASN : angle 3.08303 ( 27) link_BETA1-4 : bond 0.00478 ( 8) link_BETA1-4 : angle 2.42865 ( 24) hydrogen bonds : bond 0.03423 ( 222) hydrogen bonds : angle 5.28005 ( 624) SS BOND : bond 0.00513 ( 10) SS BOND : angle 1.08246 ( 20) covalent geometry : bond 0.00443 ( 6717) covalent geometry : angle 0.64781 ( 9155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7370 (mp10) outliers start: 30 outliers final: 17 residues processed: 121 average time/residue: 0.1470 time to fit residues: 24.9980 Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN D 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108722 restraints weight = 10987.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109562 restraints weight = 7877.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110700 restraints weight = 6138.563| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6744 Z= 0.146 Angle : 0.632 7.076 9226 Z= 0.306 Chirality : 0.046 0.358 1073 Planarity : 0.004 0.035 1157 Dihedral : 8.994 55.133 1220 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.45 % Allowed : 28.53 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.29), residues: 796 helix: -1.10 (0.81), residues: 35 sheet: -0.11 (0.29), residues: 337 loop : -0.78 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 149 HIS 0.004 0.001 HIS D 371 PHE 0.007 0.001 PHE E 387 TYR 0.007 0.001 TYR A 185 ARG 0.003 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 9) link_NAG-ASN : angle 3.00108 ( 27) link_BETA1-4 : bond 0.00454 ( 8) link_BETA1-4 : angle 2.24669 ( 24) hydrogen bonds : bond 0.03119 ( 222) hydrogen bonds : angle 5.05033 ( 624) SS BOND : bond 0.00360 ( 10) SS BOND : angle 0.91205 ( 20) covalent geometry : bond 0.00339 ( 6717) covalent geometry : angle 0.60106 ( 9155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7791 (tppt) cc_final: 0.7550 (tppt) REVERT: D 132 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: D 306 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8448 (mp) REVERT: E 184 HIS cc_start: 0.7936 (m90) cc_final: 0.7641 (m90) REVERT: E 221 LEU cc_start: 0.8511 (tp) cc_final: 0.8192 (tp) outliers start: 39 outliers final: 24 residues processed: 135 average time/residue: 0.1392 time to fit residues: 26.9386 Evaluate side-chains 117 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106535 restraints weight = 10975.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108403 restraints weight = 7991.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109662 restraints weight = 5990.239| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6744 Z= 0.168 Angle : 0.639 7.546 9226 Z= 0.308 Chirality : 0.046 0.365 1073 Planarity : 0.004 0.034 1157 Dihedral : 7.964 46.779 1218 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.73 % Allowed : 28.39 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.30), residues: 796 helix: -0.82 (0.83), residues: 36 sheet: -0.09 (0.29), residues: 334 loop : -0.72 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 149 HIS 0.004 0.001 HIS D 371 PHE 0.007 0.001 PHE D 385 TYR 0.008 0.001 TYR A 185 ARG 0.003 0.000 ARG D 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 9) link_NAG-ASN : angle 2.99761 ( 27) link_BETA1-4 : bond 0.00411 ( 8) link_BETA1-4 : angle 2.32230 ( 24) hydrogen bonds : bond 0.02949 ( 222) hydrogen bonds : angle 4.91066 ( 624) SS BOND : bond 0.00295 ( 10) SS BOND : angle 0.83443 ( 20) covalent geometry : bond 0.00396 ( 6717) covalent geometry : angle 0.60759 ( 9155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7836 (tppt) cc_final: 0.7615 (tppt) REVERT: D 132 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: D 390 LEU cc_start: 0.8252 (tt) cc_final: 0.7915 (tt) REVERT: E 221 LEU cc_start: 0.8543 (tp) cc_final: 0.8172 (tp) outliers start: 41 outliers final: 33 residues processed: 133 average time/residue: 0.1459 time to fit residues: 27.4429 Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101136 restraints weight = 10760.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104225 restraints weight = 6453.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106278 restraints weight = 4739.374| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 6744 Z= 0.223 Angle : 0.670 8.485 9226 Z= 0.326 Chirality : 0.047 0.358 1073 Planarity : 0.004 0.035 1157 Dihedral : 7.891 49.989 1218 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 6.57 % Allowed : 26.71 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 796 helix: -0.35 (0.89), residues: 36 sheet: 0.05 (0.29), residues: 317 loop : -0.73 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 149 HIS 0.004 0.001 HIS A 133 PHE 0.007 0.001 PHE E 385 TYR 0.009 0.002 TYR A 175 ARG 0.003 0.000 ARG D 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 9) link_NAG-ASN : angle 3.13041 ( 27) link_BETA1-4 : bond 0.00364 ( 8) link_BETA1-4 : angle 2.36619 ( 24) hydrogen bonds : bond 0.03090 ( 222) hydrogen bonds : angle 5.01765 ( 624) SS BOND : bond 0.00385 ( 10) SS BOND : angle 0.90080 ( 20) covalent geometry : bond 0.00529 ( 6717) covalent geometry : angle 0.63847 ( 9155) *********************** 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 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7917 (tppt) cc_final: 0.7694 (tppt) REVERT: A 94 GLN cc_start: 0.8031 (tt0) cc_final: 0.7796 (tt0) REVERT: D 132 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: E 184 HIS cc_start: 0.8107 (m90) cc_final: 0.7790 (m90) outliers start: 47 outliers final: 37 residues processed: 130 average time/residue: 0.1499 time to fit residues: 27.5570 Evaluate side-chains 121 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104382 restraints weight = 10599.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104724 restraints weight = 8789.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106176 restraints weight = 6423.664| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6744 Z= 0.163 Angle : 0.640 7.656 9226 Z= 0.311 Chirality : 0.046 0.343 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.546 46.011 1218 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 6.29 % Allowed : 26.43 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.29), residues: 796 helix: 0.09 (0.89), residues: 35 sheet: -0.08 (0.29), residues: 331 loop : -0.77 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 149 HIS 0.003 0.001 HIS D 303 PHE 0.009 0.001 PHE D 385 TYR 0.010 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 9) link_NAG-ASN : angle 3.00176 ( 27) link_BETA1-4 : bond 0.00410 ( 8) link_BETA1-4 : angle 2.22190 ( 24) hydrogen bonds : bond 0.02852 ( 222) hydrogen bonds : angle 4.93870 ( 624) SS BOND : bond 0.00208 ( 10) SS BOND : angle 0.78755 ( 20) covalent geometry : bond 0.00384 ( 6717) covalent geometry : angle 0.60935 ( 9155) *********************** 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 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7920 (tppt) cc_final: 0.7714 (tppt) REVERT: D 132 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: E 221 LEU cc_start: 0.8554 (tp) cc_final: 0.8243 (tp) REVERT: E 398 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6339 (mp0) outliers start: 45 outliers final: 34 residues processed: 132 average time/residue: 0.1832 time to fit residues: 34.0187 Evaluate side-chains 127 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 398 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.138474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102635 restraints weight = 10717.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105789 restraints weight = 6364.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107802 restraints weight = 4644.230| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6744 Z= 0.163 Angle : 0.637 7.510 9226 Z= 0.309 Chirality : 0.046 0.336 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.175 42.590 1218 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 6.29 % Allowed : 27.55 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.30), residues: 796 helix: 0.05 (0.89), residues: 35 sheet: -0.06 (0.29), residues: 331 loop : -0.72 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 64 HIS 0.002 0.001 HIS A 66 PHE 0.009 0.001 PHE D 385 TYR 0.013 0.001 TYR A 185 ARG 0.002 0.000 ARG D 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 9) link_NAG-ASN : angle 2.95550 ( 27) link_BETA1-4 : bond 0.00384 ( 8) link_BETA1-4 : angle 2.19700 ( 24) hydrogen bonds : bond 0.02842 ( 222) hydrogen bonds : angle 4.92284 ( 624) SS BOND : bond 0.00238 ( 10) SS BOND : angle 0.75566 ( 20) covalent geometry : bond 0.00388 ( 6717) covalent geometry : angle 0.60781 ( 9155) *********************** 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 146 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: D 185 TRP cc_start: 0.8910 (t-100) cc_final: 0.8675 (t-100) outliers start: 45 outliers final: 37 residues processed: 136 average time/residue: 0.1478 time to fit residues: 28.8876 Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 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 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.137590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101979 restraints weight = 10785.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105115 restraints weight = 6439.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107161 restraints weight = 4706.035| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6744 Z= 0.181 Angle : 0.650 7.810 9226 Z= 0.317 Chirality : 0.046 0.334 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.169 41.465 1218 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.73 % Allowed : 28.11 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.30), residues: 796 helix: 0.17 (0.91), residues: 34 sheet: -0.11 (0.28), residues: 333 loop : -0.68 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 149 HIS 0.002 0.001 HIS D 409 PHE 0.008 0.001 PHE D 385 TYR 0.014 0.002 TYR A 185 ARG 0.002 0.000 ARG E 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 9) link_NAG-ASN : angle 2.97979 ( 27) link_BETA1-4 : bond 0.00355 ( 8) link_BETA1-4 : angle 2.23876 ( 24) hydrogen bonds : bond 0.02844 ( 222) hydrogen bonds : angle 4.95358 ( 624) SS BOND : bond 0.00238 ( 10) SS BOND : angle 0.91275 ( 20) covalent geometry : bond 0.00431 ( 6717) covalent geometry : angle 0.62052 ( 9155) *********************** 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 141 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: D 185 TRP cc_start: 0.8991 (t-100) cc_final: 0.8719 (t-100) REVERT: E 391 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.7010 (mt-10) outliers start: 41 outliers final: 36 residues processed: 134 average time/residue: 0.1440 time to fit residues: 27.0804 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 0.0570 chunk 18 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104211 restraints weight = 10798.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107397 restraints weight = 6362.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109460 restraints weight = 4602.754| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6744 Z= 0.127 Angle : 0.629 8.109 9226 Z= 0.303 Chirality : 0.045 0.320 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.712 40.047 1218 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.31 % Allowed : 28.67 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.30), residues: 796 helix: 0.15 (0.90), residues: 34 sheet: -0.10 (0.29), residues: 335 loop : -0.60 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 149 HIS 0.003 0.001 HIS E 184 PHE 0.010 0.001 PHE D 385 TYR 0.015 0.001 TYR A 185 ARG 0.002 0.000 ARG E 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 9) link_NAG-ASN : angle 2.84628 ( 27) link_BETA1-4 : bond 0.00426 ( 8) link_BETA1-4 : angle 2.06313 ( 24) hydrogen bonds : bond 0.02706 ( 222) hydrogen bonds : angle 4.88178 ( 624) SS BOND : bond 0.00199 ( 10) SS BOND : angle 0.96872 ( 20) covalent geometry : bond 0.00301 ( 6717) covalent geometry : angle 0.60157 ( 9155) *********************** 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 141 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 TYR cc_start: 0.9081 (p90) cc_final: 0.8866 (p90) REVERT: D 132 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: E 206 THR cc_start: 0.8371 (p) cc_final: 0.8171 (p) outliers start: 38 outliers final: 34 residues processed: 133 average time/residue: 0.1520 time to fit residues: 28.2630 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 : 0.739 ------------------------------------------------------------------------------- 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 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101044 restraints weight = 10905.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104158 restraints weight = 6552.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106142 restraints weight = 4791.010| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 6744 Z= 0.225 Angle : 0.686 8.462 9226 Z= 0.332 Chirality : 0.047 0.335 1073 Planarity : 0.004 0.033 1157 Dihedral : 7.157 41.645 1218 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.59 % Allowed : 27.83 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 796 helix: -0.81 (0.83), residues: 40 sheet: 0.05 (0.29), residues: 325 loop : -0.60 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 185 HIS 0.003 0.001 HIS E 184 PHE 0.007 0.001 PHE E 385 TYR 0.019 0.002 TYR A 185 ARG 0.006 0.000 ARG E 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 9) link_NAG-ASN : angle 3.06086 ( 27) link_BETA1-4 : bond 0.00305 ( 8) link_BETA1-4 : angle 2.36556 ( 24) hydrogen bonds : bond 0.02994 ( 222) hydrogen bonds : angle 5.02554 ( 624) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.04733 ( 20) covalent geometry : bond 0.00538 ( 6717) covalent geometry : angle 0.65550 ( 9155) ********************** 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 133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8190 (tt0) cc_final: 0.7964 (tm-30) REVERT: D 132 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: E 391 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6989 (mt-10) outliers start: 40 outliers final: 34 residues processed: 124 average time/residue: 0.1466 time to fit residues: 25.8620 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 126 HIS Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 305 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.0770 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103086 restraints weight = 10979.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106316 restraints weight = 6462.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108350 restraints weight = 4673.958| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6744 Z= 0.146 Angle : 0.652 8.810 9226 Z= 0.314 Chirality : 0.048 0.431 1073 Planarity : 0.004 0.033 1157 Dihedral : 6.811 40.633 1216 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.31 % Allowed : 28.11 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.30), residues: 796 helix: 0.11 (0.90), residues: 34 sheet: -0.13 (0.29), residues: 336 loop : -0.56 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 185 HIS 0.003 0.001 HIS E 184 PHE 0.009 0.001 PHE D 385 TYR 0.029 0.001 TYR A 185 ARG 0.004 0.000 ARG E 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 9) link_NAG-ASN : angle 3.24673 ( 27) link_BETA1-4 : bond 0.00389 ( 8) link_BETA1-4 : angle 2.12101 ( 24) hydrogen bonds : bond 0.02778 ( 222) hydrogen bonds : angle 4.94781 ( 624) SS BOND : bond 0.00206 ( 10) SS BOND : angle 0.97678 ( 20) covalent geometry : bond 0.00346 ( 6717) covalent geometry : angle 0.61916 ( 9155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.76 seconds wall clock time: 41 minutes 17.61 seconds (2477.61 seconds total)