Starting phenix.real_space_refine on Thu Jul 2 06:17:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.map" model { file = "/net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n64_24193/07_2026/7n64_24193.cif" } resolution = 4.2 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= 0.002 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 26 5.16 5 C 4574 2.51 5 N 1194 2.21 5 O 1395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7189 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2235 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1687 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1604 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "F" 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 chiralities: 2 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 chiralities: 3 Chain: "A" 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 chiralities: 2 Time building chain proxies: 1.66, per 1000 atoms: 0.23 Number of scatterers: 7189 At special positions: 0 Unit cell: (99, 79.2, 120.45, 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 26 16.00 O 1395 8.00 N 1194 7.00 C 4574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 160 " - pdb=" SG CYS H 216 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 165 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN B 343 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 321.0 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 6.3% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.708A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 59 through 63 removed outlier: 3.853A pdb=" N LYS H 63 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 209 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.300A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 7.424A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.168A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 121 Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.779A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.685A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.087A pdb=" N SER H 69 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 47 through 50 removed outlier: 5.264A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR H 92 " --> pdb=" O THR H 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.506A pdb=" N LYS H 163 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR H 196 " --> pdb=" O ASP H 164 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER H 199 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 171 through 174 removed outlier: 3.833A pdb=" N TYR H 214 " --> pdb=" O VAL H 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.581A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 118 removed outlier: 4.729A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE L 139 " --> pdb=" O TYR L 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 144 through 149 187 hydrogen bonds defined for protein. 444 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: 0.90 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1932 1.33 - 1.45: 1675 1.45 - 1.57: 3736 1.57 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 7375 Sorted by residual: bond pdb=" N GLN L 3 " pdb=" CA GLN L 3 " ideal model delta sigma weight residual 1.452 1.504 -0.051 1.22e-02 6.72e+03 1.76e+01 bond pdb=" C ALA L 111 " pdb=" N ALA L 112 " ideal model delta sigma weight residual 1.333 1.240 0.093 2.74e-02 1.33e+03 1.14e+01 bond pdb=" N GLN L 100 " pdb=" CA GLN L 100 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.17e-02 7.31e+03 9.83e+00 bond pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.27e-02 6.20e+03 9.03e+00 bond pdb=" N ARG A 237 " pdb=" CA ARG A 237 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.13e-02 7.83e+03 8.78e+00 ... (remaining 7370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 9485 2.24 - 4.48: 497 4.48 - 6.72: 44 6.72 - 8.97: 7 8.97 - 11.21: 2 Bond angle restraints: 10035 Sorted by residual: angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 117.47 123.32 -5.85 1.16e+00 7.43e-01 2.55e+01 angle pdb=" C ILE L 106 " pdb=" N LYS L 107 " pdb=" CA LYS L 107 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C TYR A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta sigma weight residual 122.10 116.05 6.05 1.66e+00 3.63e-01 1.33e+01 angle pdb=" N GLN L 124 " pdb=" CA GLN L 124 " pdb=" C GLN L 124 " ideal model delta sigma weight residual 111.07 107.30 3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N SER B 371 " pdb=" CA SER B 371 " pdb=" C SER B 371 " ideal model delta sigma weight residual 114.56 110.16 4.40 1.27e+00 6.20e-01 1.20e+01 ... (remaining 10030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 3696 16.06 - 32.13: 474 32.13 - 48.19: 93 48.19 - 64.25: 27 64.25 - 80.32: 10 Dihedral angle restraints: 4300 sinusoidal: 1670 harmonic: 2630 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 149.28 -56.28 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS H 160 " pdb=" SG CYS H 160 " pdb=" SG CYS H 216 " pdb=" CB CYS H 216 " ideal model delta sinusoidal sigma weight residual 93.00 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 4297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 981 0.091 - 0.181: 121 0.181 - 0.272: 11 0.272 - 0.362: 1 0.362 - 0.453: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CB VAL A 130 " pdb=" CA VAL A 130 " pdb=" CG1 VAL A 130 " pdb=" CG2 VAL A 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1113 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 138 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO H 139 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO H 139 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 139 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 368 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C LEU B 368 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU B 368 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR B 369 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 148 " 0.015 2.00e-02 2.50e+03 1.63e-02 6.64e+00 pdb=" CG TRP L 148 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP L 148 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 148 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 148 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 148 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP L 148 " -0.000 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 553 2.71 - 3.25: 7847 3.25 - 3.80: 11838 3.80 - 4.35: 14933 4.35 - 4.90: 24653 Nonbonded interactions: 59824 Sorted by model distance: nonbonded pdb=" O ASN H 53 " pdb=" OG SER H 54 " model vdw 2.157 3.040 nonbonded pdb=" CG2 ILE L 2 " pdb=" N GLN L 3 " model vdw 2.193 3.540 nonbonded pdb=" N GLY B 404 " pdb=" O GLN B 506 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.211 3.120 nonbonded pdb=" N GLN H 191 " pdb=" O LEU H 195 " model vdw 2.216 3.120 ... (remaining 59819 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.060 Find NCS groups from input model: 0.040 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 : 0.009 0.093 7392 Z= 0.430 Angle : 1.095 12.851 10076 Z= 0.594 Chirality : 0.062 0.453 1116 Planarity : 0.006 0.072 1286 Dihedral : 15.214 80.315 2590 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 36.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 20.76 % Favored : 78.91 % Rotamer: Outliers : 1.78 % Allowed : 1.40 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.80 (0.26), residues: 896 helix: -3.80 (0.50), residues: 40 sheet: -1.47 (0.32), residues: 269 loop : -3.15 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.034 0.003 TYR H 93 PHE 0.036 0.004 PHE B 377 TRP 0.042 0.004 TRP L 148 HIS 0.008 0.002 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.43 ( 7375) covalent geometry : angle 1.05984 / 0.59 (10035) SS BOND : bond 0.00803 / 0.44 ( 10) SS BOND : angle 2.67776 / 1.98 ( 20) hydrogen bonds : bond 0.13764 / 9.43 ( 181) hydrogen bonds : angle 9.33386 / 6.50 ( 444) link_BETA1-4 : bond 0.00687 / 0.35 ( 3) link_BETA1-4 : angle 4.96916 / 2.66 ( 9) link_NAG-ASN : bond 0.00939 / 0.47 ( 4) link_NAG-ASN : angle 6.06386 / 3.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7737 (ptmm) cc_final: 0.7101 (ptmm) REVERT: A 224 GLU cc_start: 0.7897 (pm20) cc_final: 0.7502 (pm20) REVERT: L 138 ASN cc_start: 0.8587 (m110) cc_final: 0.7973 (m110) REVERT: L 192 TYR cc_start: 0.6668 (m-80) cc_final: 0.6386 (m-10) outliers start: 14 outliers final: 5 residues processed: 167 average time/residue: 0.0691 time to fit residues: 15.4288 Evaluate side-chains 126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 147 GLN L 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.131208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108257 restraints weight = 17794.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110948 restraints weight = 10272.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112733 restraints weight = 6915.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113997 restraints weight = 5228.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114705 restraints weight = 4244.117| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7392 Z= 0.172 Angle : 0.843 13.492 10076 Z= 0.423 Chirality : 0.051 0.254 1116 Planarity : 0.006 0.052 1286 Dihedral : 6.799 24.724 985 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 0.13 % Allowed : 9.01 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.39 (0.27), residues: 896 helix: -3.72 (0.47), residues: 39 sheet: -1.43 (0.31), residues: 293 loop : -2.74 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.038 0.002 TYR L 91 PHE 0.016 0.002 PHE B 497 TRP 0.021 0.002 TRP L 148 HIS 0.005 0.001 HIS H 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 7375) covalent geometry : angle 0.81597 / 0.42 (10035) SS BOND : bond 0.00346 / 0.17 ( 10) SS BOND : angle 1.42672 / 1.08 ( 20) hydrogen bonds : bond 0.04039 / 2.78 ( 181) hydrogen bonds : angle 7.89901 / 5.45 ( 444) link_BETA1-4 : bond 0.00685 / 0.35 ( 3) link_BETA1-4 : angle 3.09351 / 1.61 ( 9) link_NAG-ASN : bond 0.00563 / 0.28 ( 4) link_NAG-ASN : angle 5.46690 / 3.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7502 (p) cc_final: 0.6624 (p) REVERT: A 206 LYS cc_start: 0.7982 (ptmm) cc_final: 0.7521 (ptmm) REVERT: A 224 GLU cc_start: 0.7695 (pm20) cc_final: 0.7388 (pm20) REVERT: B 360 ASN cc_start: 0.8357 (t0) cc_final: 0.8124 (t0) REVERT: B 466 ARG cc_start: 0.7666 (ttp80) cc_final: 0.6704 (ttt-90) REVERT: B 516 GLU cc_start: 0.8228 (tp30) cc_final: 0.7938 (tm-30) REVERT: H 87 GLU cc_start: 0.8384 (pm20) cc_final: 0.8136 (pm20) REVERT: L 4 MET cc_start: 0.6761 (tpt) cc_final: 0.6275 (tpt) REVERT: L 21 ILE cc_start: 0.6901 (tp) cc_final: 0.6436 (mp) REVERT: L 91 TYR cc_start: 0.7360 (p90) cc_final: 0.6638 (p90) REVERT: L 138 ASN cc_start: 0.8670 (m110) cc_final: 0.8220 (m110) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.0671 time to fit residues: 14.4288 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.132229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109279 restraints weight = 17394.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.111915 restraints weight = 10081.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113709 restraints weight = 6852.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.114960 restraints weight = 5183.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.115774 restraints weight = 4229.520| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7392 Z= 0.173 Angle : 0.821 14.369 10076 Z= 0.408 Chirality : 0.050 0.289 1116 Planarity : 0.005 0.049 1286 Dihedral : 6.581 25.211 985 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.27), residues: 896 helix: -3.31 (0.59), residues: 39 sheet: -1.40 (0.30), residues: 306 loop : -2.62 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.033 0.002 TYR L 192 PHE 0.027 0.002 PHE B 347 TRP 0.025 0.002 TRP H 174 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 7375) covalent geometry : angle 0.79333 / 0.40 (10035) SS BOND : bond 0.00344 / 0.17 ( 10) SS BOND : angle 1.24928 / 0.97 ( 20) hydrogen bonds : bond 0.04021 / 2.77 ( 181) hydrogen bonds : angle 7.66082 / 5.27 ( 444) link_BETA1-4 : bond 0.00610 / 0.31 ( 3) link_BETA1-4 : angle 2.80529 / 1.49 ( 9) link_NAG-ASN : bond 0.00678 / 0.34 ( 4) link_NAG-ASN : angle 5.54164 / 3.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8136 (tp) cc_final: 0.7864 (tp) REVERT: A 191 GLU cc_start: 0.5826 (mm-30) cc_final: 0.5553 (mm-30) REVERT: A 206 LYS cc_start: 0.8017 (ptmm) cc_final: 0.7773 (ptmm) REVERT: A 242 LEU cc_start: 0.7296 (mp) cc_final: 0.6815 (mt) REVERT: A 279 TYR cc_start: 0.5499 (m-80) cc_final: 0.5098 (m-80) REVERT: B 360 ASN cc_start: 0.8397 (t0) cc_final: 0.8178 (t0) REVERT: B 405 ASP cc_start: 0.8065 (p0) cc_final: 0.7827 (p0) REVERT: B 466 ARG cc_start: 0.7684 (ttp80) cc_final: 0.6630 (ttt-90) REVERT: B 487 ASN cc_start: 0.5414 (t0) cc_final: 0.5195 (t0) REVERT: B 516 GLU cc_start: 0.8101 (tp30) cc_final: 0.7833 (tm-30) REVERT: H 31 ASP cc_start: 0.6800 (m-30) cc_final: 0.6515 (m-30) REVERT: H 87 GLU cc_start: 0.8446 (pm20) cc_final: 0.8116 (pm20) REVERT: L 4 MET cc_start: 0.6461 (tpt) cc_final: 0.6081 (tpt) REVERT: L 138 ASN cc_start: 0.8689 (m110) cc_final: 0.8094 (m110) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0742 time to fit residues: 15.7667 Evaluate side-chains 134 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN L 124 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.134634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111345 restraints weight = 17536.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.114126 restraints weight = 10113.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115992 restraints weight = 6766.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117251 restraints weight = 5077.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.118011 restraints weight = 4156.243| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7392 Z= 0.146 Angle : 0.779 14.196 10076 Z= 0.387 Chirality : 0.048 0.272 1116 Planarity : 0.005 0.051 1286 Dihedral : 6.335 24.915 985 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.07 (0.28), residues: 896 helix: -3.68 (0.59), residues: 33 sheet: -1.18 (0.31), residues: 294 loop : -2.54 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.016 0.002 TYR L 192 PHE 0.017 0.002 PHE B 347 TRP 0.022 0.001 TRP L 148 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 7375) covalent geometry : angle 0.75212 / 0.38 (10035) SS BOND : bond 0.00248 / 0.14 ( 10) SS BOND : angle 1.08067 / 0.84 ( 20) hydrogen bonds : bond 0.03644 / 2.42 ( 181) hydrogen bonds : angle 7.38982 / 5.05 ( 444) link_BETA1-4 : bond 0.00671 / 0.34 ( 3) link_BETA1-4 : angle 2.64919 / 1.43 ( 9) link_NAG-ASN : bond 0.00693 / 0.35 ( 4) link_NAG-ASN : angle 5.35298 / 3.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.5403 (m-80) cc_final: 0.5126 (m-80) REVERT: B 360 ASN cc_start: 0.8358 (t0) cc_final: 0.8157 (t0) REVERT: B 466 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6635 (ttt-90) REVERT: B 487 ASN cc_start: 0.5519 (t0) cc_final: 0.5288 (t0) REVERT: H 19 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8070 (ttp80) REVERT: H 31 ASP cc_start: 0.6874 (m-30) cc_final: 0.6609 (m-30) REVERT: H 87 GLU cc_start: 0.8470 (pm20) cc_final: 0.8070 (pm20) REVERT: H 181 SER cc_start: 0.7501 (t) cc_final: 0.7143 (m) REVERT: L 4 MET cc_start: 0.6481 (tpt) cc_final: 0.6010 (tpt) REVERT: L 82 ASP cc_start: 0.8383 (m-30) cc_final: 0.7235 (m-30) REVERT: L 138 ASN cc_start: 0.8566 (m110) cc_final: 0.8046 (m110) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0701 time to fit residues: 16.6910 Evaluate side-chains 133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 76 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3922 r_free = 0.3922 target = 0.134134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110762 restraints weight = 17466.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113305 restraints weight = 10204.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115083 restraints weight = 7010.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116224 restraints weight = 5315.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116947 restraints weight = 4407.573| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7392 Z= 0.167 Angle : 0.785 14.131 10076 Z= 0.392 Chirality : 0.049 0.271 1116 Planarity : 0.005 0.049 1286 Dihedral : 6.232 23.359 985 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.01 (0.28), residues: 896 helix: -3.89 (0.59), residues: 33 sheet: -1.14 (0.31), residues: 297 loop : -2.50 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.016 0.002 TYR B 505 PHE 0.021 0.002 PHE B 497 TRP 0.031 0.002 TRP H 174 HIS 0.004 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 7375) covalent geometry : angle 0.75861 / 0.39 (10035) SS BOND : bond 0.00318 / 0.16 ( 10) SS BOND : angle 1.26506 / 0.90 ( 20) hydrogen bonds : bond 0.03584 / 2.39 ( 181) hydrogen bonds : angle 7.25545 / 4.96 ( 444) link_BETA1-4 : bond 0.00590 / 0.30 ( 3) link_BETA1-4 : angle 2.55611 / 1.40 ( 9) link_NAG-ASN : bond 0.00600 / 0.30 ( 4) link_NAG-ASN : angle 5.39191 / 3.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7359 (mp0) cc_final: 0.7119 (mm-30) REVERT: A 206 LYS cc_start: 0.7931 (ptmm) cc_final: 0.7713 (ptmm) REVERT: A 279 TYR cc_start: 0.5392 (m-80) cc_final: 0.4875 (m-80) REVERT: A 287 ASP cc_start: 0.7392 (p0) cc_final: 0.7153 (p0) REVERT: B 360 ASN cc_start: 0.8402 (t0) cc_final: 0.8181 (t0) REVERT: B 466 ARG cc_start: 0.7710 (ttp80) cc_final: 0.6672 (ttt180) REVERT: B 487 ASN cc_start: 0.5862 (t0) cc_final: 0.5610 (t0) REVERT: B 505 TYR cc_start: 0.7054 (m-80) cc_final: 0.6597 (m-80) REVERT: H 19 ARG cc_start: 0.8455 (ttp80) cc_final: 0.7828 (ttp80) REVERT: H 31 ASP cc_start: 0.7006 (m-30) cc_final: 0.6453 (m-30) REVERT: H 87 GLU cc_start: 0.8464 (pm20) cc_final: 0.8097 (pm20) REVERT: H 181 SER cc_start: 0.7542 (t) cc_final: 0.7195 (m) REVERT: H 224 ASN cc_start: 0.8242 (m-40) cc_final: 0.7395 (p0) REVERT: L 4 MET cc_start: 0.6465 (tpt) cc_final: 0.6007 (tpt) REVERT: L 21 ILE cc_start: 0.6344 (tp) cc_final: 0.5707 (mp) REVERT: L 91 TYR cc_start: 0.6924 (p90) cc_final: 0.6701 (p90) REVERT: L 138 ASN cc_start: 0.8627 (m110) cc_final: 0.7929 (m110) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0676 time to fit residues: 15.4510 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 84 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS A 146 HIS A 148 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.136449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112590 restraints weight = 17325.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115362 restraints weight = 10009.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.117175 restraints weight = 6761.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118413 restraints weight = 5116.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119111 restraints weight = 4181.193| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7392 Z= 0.144 Angle : 0.769 13.591 10076 Z= 0.381 Chirality : 0.049 0.270 1116 Planarity : 0.006 0.051 1286 Dihedral : 6.028 22.677 985 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.91 (0.28), residues: 896 helix: -3.92 (0.58), residues: 33 sheet: -1.08 (0.30), residues: 302 loop : -2.41 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.013 0.002 TYR H 78 PHE 0.020 0.002 PHE B 497 TRP 0.021 0.001 TRP L 148 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7375) covalent geometry : angle 0.74307 / 0.38 (10035) SS BOND : bond 0.00249 / 0.14 ( 10) SS BOND : angle 1.34967 / 0.91 ( 20) hydrogen bonds : bond 0.03512 / 2.34 ( 181) hydrogen bonds : angle 7.05230 / 4.81 ( 444) link_BETA1-4 : bond 0.00797 / 0.40 ( 3) link_BETA1-4 : angle 2.59098 / 1.41 ( 9) link_NAG-ASN : bond 0.00662 / 0.33 ( 4) link_NAG-ASN : angle 5.12078 / 3.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7389 (mp0) cc_final: 0.6864 (mm-30) REVERT: A 206 LYS cc_start: 0.7931 (ptmm) cc_final: 0.7662 (ptmm) REVERT: A 287 ASP cc_start: 0.7490 (p0) cc_final: 0.7050 (p0) REVERT: B 466 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6665 (ttt180) REVERT: B 487 ASN cc_start: 0.5685 (t0) cc_final: 0.5325 (t0) REVERT: H 31 ASP cc_start: 0.7002 (m-30) cc_final: 0.6424 (m-30) REVERT: H 87 GLU cc_start: 0.8490 (pm20) cc_final: 0.8115 (pm20) REVERT: H 190 LEU cc_start: 0.8391 (tp) cc_final: 0.7775 (mp) REVERT: H 224 ASN cc_start: 0.8251 (m-40) cc_final: 0.7452 (p0) REVERT: L 4 MET cc_start: 0.6375 (tpt) cc_final: 0.6044 (tpt) REVERT: L 21 ILE cc_start: 0.6288 (tp) cc_final: 0.5655 (mp) REVERT: L 91 TYR cc_start: 0.6864 (p90) cc_final: 0.6531 (p90) REVERT: L 138 ASN cc_start: 0.8587 (m110) cc_final: 0.7853 (m110) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0703 time to fit residues: 16.2569 Evaluate side-chains 129 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3887 r_free = 0.3887 target = 0.131545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108282 restraints weight = 17609.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110846 restraints weight = 10416.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112544 restraints weight = 7110.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113677 restraints weight = 5412.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.114329 restraints weight = 4492.604| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7392 Z= 0.232 Angle : 0.850 14.022 10076 Z= 0.426 Chirality : 0.051 0.309 1116 Planarity : 0.006 0.051 1286 Dihedral : 6.455 24.990 985 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.98 (0.27), residues: 896 helix: -3.27 (0.65), residues: 39 sheet: -1.02 (0.32), residues: 279 loop : -2.52 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.025 0.003 TYR L 140 PHE 0.029 0.003 PHE A 275 TRP 0.047 0.003 TRP H 174 HIS 0.006 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 ( 7375) covalent geometry : angle 0.82254 / 0.42 (10035) SS BOND : bond 0.00399 / 0.21 ( 10) SS BOND : angle 1.81463 / 1.46 ( 20) hydrogen bonds : bond 0.03926 / 2.67 ( 181) hydrogen bonds : angle 7.29389 / 5.02 ( 444) link_BETA1-4 : bond 0.00529 / 0.27 ( 3) link_BETA1-4 : angle 2.45318 / 1.41 ( 9) link_NAG-ASN : bond 0.00767 / 0.38 ( 4) link_NAG-ASN : angle 5.55312 / 3.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7973 (ptmm) cc_final: 0.7695 (ptmm) REVERT: B 360 ASN cc_start: 0.8380 (t0) cc_final: 0.8171 (t0) REVERT: B 466 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7040 (ptm160) REVERT: B 487 ASN cc_start: 0.5999 (t0) cc_final: 0.5643 (t0) REVERT: H 6 GLU cc_start: 0.8816 (mp0) cc_final: 0.8344 (mp0) REVERT: H 31 ASP cc_start: 0.7102 (m-30) cc_final: 0.6674 (m-30) REVERT: H 51 ILE cc_start: 0.9105 (tt) cc_final: 0.8876 (tt) REVERT: H 87 GLU cc_start: 0.8507 (pm20) cc_final: 0.8127 (pm20) REVERT: L 21 ILE cc_start: 0.6398 (tp) cc_final: 0.5792 (mp) REVERT: L 138 ASN cc_start: 0.8680 (m110) cc_final: 0.7906 (m110) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0753 time to fit residues: 16.0741 Evaluate side-chains 129 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.133767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110572 restraints weight = 17327.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113163 restraints weight = 9968.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114959 restraints weight = 6780.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.116165 restraints weight = 5109.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.116877 restraints weight = 4178.965| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7392 Z= 0.182 Angle : 0.813 13.922 10076 Z= 0.406 Chirality : 0.050 0.301 1116 Planarity : 0.005 0.045 1286 Dihedral : 6.357 26.200 985 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.93 (0.27), residues: 896 helix: -3.82 (0.61), residues: 33 sheet: -0.94 (0.32), residues: 282 loop : -2.50 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.026 0.002 TYR L 140 PHE 0.031 0.002 PHE B 497 TRP 0.025 0.002 TRP L 148 HIS 0.008 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 7375) covalent geometry : angle 0.78640 / 0.40 (10035) SS BOND : bond 0.00386 / 0.19 ( 10) SS BOND : angle 1.71390 / 1.42 ( 20) hydrogen bonds : bond 0.03554 / 2.39 ( 181) hydrogen bonds : angle 7.10288 / 4.85 ( 444) link_BETA1-4 : bond 0.00714 / 0.36 ( 3) link_BETA1-4 : angle 2.46098 / 1.37 ( 9) link_NAG-ASN : bond 0.00714 / 0.36 ( 4) link_NAG-ASN : angle 5.35019 / 3.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7688 (ptmm) REVERT: B 406 GLU cc_start: 0.8491 (mp0) cc_final: 0.7855 (mt-10) REVERT: B 466 ARG cc_start: 0.7754 (ttp80) cc_final: 0.6923 (ptm160) REVERT: B 487 ASN cc_start: 0.5852 (t0) cc_final: 0.5475 (t0) REVERT: H 31 ASP cc_start: 0.7098 (m-30) cc_final: 0.6762 (m-30) REVERT: H 51 ILE cc_start: 0.9105 (tt) cc_final: 0.8895 (tt) REVERT: H 87 GLU cc_start: 0.8530 (pm20) cc_final: 0.8151 (pm20) REVERT: L 4 MET cc_start: 0.6318 (tpt) cc_final: 0.5929 (tpt) REVERT: L 21 ILE cc_start: 0.6373 (tp) cc_final: 0.6141 (tp) REVERT: L 138 ASN cc_start: 0.8758 (m110) cc_final: 0.8039 (m110) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0690 time to fit residues: 15.3591 Evaluate side-chains 127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 65 optimal weight: 0.4980 chunk 2 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111518 restraints weight = 17195.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114219 restraints weight = 9916.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116051 restraints weight = 6727.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117198 restraints weight = 5087.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118101 restraints weight = 4196.796| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7392 Z= 0.157 Angle : 0.804 13.260 10076 Z= 0.399 Chirality : 0.049 0.273 1116 Planarity : 0.005 0.043 1286 Dihedral : 6.187 25.696 985 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.82 (0.28), residues: 896 helix: -3.68 (0.65), residues: 33 sheet: -1.05 (0.30), residues: 310 loop : -2.35 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 403 TYR 0.023 0.002 TYR L 140 PHE 0.046 0.002 PHE B 497 TRP 0.051 0.002 TRP H 174 HIS 0.008 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7375) covalent geometry : angle 0.77681 / 0.39 (10035) SS BOND : bond 0.00529 / 0.25 ( 10) SS BOND : angle 2.07491 / 1.50 ( 20) hydrogen bonds : bond 0.03585 / 2.35 ( 181) hydrogen bonds : angle 6.95452 / 4.74 ( 444) link_BETA1-4 : bond 0.00635 / 0.32 ( 3) link_BETA1-4 : angle 2.46497 / 1.36 ( 9) link_NAG-ASN : bond 0.00639 / 0.32 ( 4) link_NAG-ASN : angle 5.13744 / 3.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7640 (ptmm) REVERT: B 403 ARG cc_start: 0.6899 (ptm-80) cc_final: 0.6537 (ptm-80) REVERT: B 487 ASN cc_start: 0.5802 (t0) cc_final: 0.5452 (t0) REVERT: B 516 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6920 (tm-30) REVERT: H 51 ILE cc_start: 0.9092 (tt) cc_final: 0.8891 (tt) REVERT: H 87 GLU cc_start: 0.8529 (pm20) cc_final: 0.8166 (pm20) REVERT: H 186 PHE cc_start: 0.8014 (m-80) cc_final: 0.7783 (m-10) REVERT: H 224 ASN cc_start: 0.8249 (m-40) cc_final: 0.7405 (p0) REVERT: L 4 MET cc_start: 0.6397 (tpt) cc_final: 0.5995 (tpt) REVERT: L 138 ASN cc_start: 0.8711 (m110) cc_final: 0.7929 (m110) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0648 time to fit residues: 14.9333 Evaluate side-chains 136 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111819 restraints weight = 17317.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114610 restraints weight = 9989.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116492 restraints weight = 6706.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117590 restraints weight = 5028.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.118500 restraints weight = 4151.281| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7392 Z= 0.169 Angle : 0.813 13.508 10076 Z= 0.404 Chirality : 0.050 0.289 1116 Planarity : 0.005 0.043 1286 Dihedral : 6.149 25.257 985 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.77 (0.28), residues: 896 helix: -3.09 (0.67), residues: 39 sheet: -1.00 (0.31), residues: 309 loop : -2.35 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.024 0.002 TYR L 140 PHE 0.040 0.002 PHE B 497 TRP 0.036 0.002 TRP L 35 HIS 0.008 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 7375) covalent geometry : angle 0.78609 / 0.40 (10035) SS BOND : bond 0.00359 / 0.17 ( 10) SS BOND : angle 1.96510 / 1.49 ( 20) hydrogen bonds : bond 0.03536 / 2.33 ( 181) hydrogen bonds : angle 6.91598 / 4.72 ( 444) link_BETA1-4 : bond 0.00619 / 0.31 ( 3) link_BETA1-4 : angle 2.41337 / 1.35 ( 9) link_NAG-ASN : bond 0.00680 / 0.34 ( 4) link_NAG-ASN : angle 5.18062 / 3.20 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5744 (mmt180) cc_final: 0.5101 (mmt180) REVERT: A 206 LYS cc_start: 0.7856 (ptmm) cc_final: 0.7639 (ptmm) REVERT: B 466 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7000 (ptm160) REVERT: B 487 ASN cc_start: 0.5815 (t0) cc_final: 0.5445 (t0) REVERT: B 516 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6885 (tm-30) REVERT: H 51 ILE cc_start: 0.9091 (tt) cc_final: 0.8889 (tt) REVERT: H 87 GLU cc_start: 0.8556 (pm20) cc_final: 0.8186 (pm20) REVERT: H 224 ASN cc_start: 0.8239 (m-40) cc_final: 0.7393 (p0) REVERT: L 4 MET cc_start: 0.6356 (tpt) cc_final: 0.5993 (tpt) REVERT: L 138 ASN cc_start: 0.8797 (m110) cc_final: 0.7968 (m110) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0658 time to fit residues: 14.8339 Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.131638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108127 restraints weight = 17570.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110669 restraints weight = 10287.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112416 restraints weight = 7047.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113618 restraints weight = 5371.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114275 restraints weight = 4395.592| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7392 Z= 0.239 Angle : 0.880 13.823 10076 Z= 0.439 Chirality : 0.051 0.319 1116 Planarity : 0.006 0.048 1286 Dihedral : 6.581 26.809 985 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -2.89 (0.27), residues: 896 helix: -3.58 (0.82), residues: 27 sheet: -1.09 (0.31), residues: 290 loop : -2.40 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 403 TYR 0.026 0.003 TYR L 140 PHE 0.022 0.002 PHE A 186 TRP 0.036 0.003 TRP L 148 HIS 0.008 0.002 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 ( 7375) covalent geometry : angle 0.85216 / 0.43 (10035) SS BOND : bond 0.00468 / 0.22 ( 10) SS BOND : angle 2.21318 / 1.72 ( 20) hydrogen bonds : bond 0.04155 / 2.76 ( 181) hydrogen bonds : angle 7.22495 / 4.98 ( 444) link_BETA1-4 : bond 0.00744 / 0.37 ( 3) link_BETA1-4 : angle 2.40587 / 1.43 ( 9) link_NAG-ASN : bond 0.00727 / 0.36 ( 4) link_NAG-ASN : angle 5.52975 / 3.37 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1059.03 seconds wall clock time: 19 minutes 5.32 seconds (1145.32 seconds total)