Starting phenix.real_space_refine on Thu Jul 2 00:58:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ez3_28728/07_2026/8ez3_28728.cif" } resolution = 2.5 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.123 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 3039 2.51 5 N 839 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 4894 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 371} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.33, per 1000 atoms: 0.27 Number of scatterers: 4894 At special positions: 0 Unit cell: (96.46, 80.56, 93.28, 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 990 8.00 N 839 7.00 C 3039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 177.4 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.5% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'L' and resid 27B through 30 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.651A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.642A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.054A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.396A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.511A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.820A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.167A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.858A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.624A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.249A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.514A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 441 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: 0.80 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1596 1.35 - 1.48: 1352 1.48 - 1.60: 2030 1.60 - 1.73: 0 1.73 - 1.85: 30 Bond restraints: 5008 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.449 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C2 BMA B 3 " pdb=" C3 BMA B 3 " ideal model delta sigma weight residual 1.544 1.513 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C5 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 5003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 6738 2.57 - 5.15: 62 5.15 - 7.72: 9 7.72 - 10.29: 0 10.29 - 12.86: 1 Bond angle restraints: 6810 Sorted by residual: angle pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " pdb=" SG CYS A 417 " ideal model delta sigma weight residual 114.40 127.26 -12.86 2.30e+00 1.89e-01 3.13e+01 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C HIS A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C CYS A 417 " pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sigma weight residual 109.68 115.29 -5.61 1.98e+00 2.55e-01 8.04e+00 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.70 126.41 -4.71 1.80e+00 3.09e-01 6.86e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2499 17.91 - 35.81: 287 35.81 - 53.72: 84 53.72 - 71.62: 16 71.62 - 89.53: 8 Dihedral angle restraints: 2894 sinusoidal: 1128 harmonic: 1766 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 135.77 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 50.93 42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA ASN L 51 " pdb=" C ASN L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 2891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 604 0.052 - 0.105: 135 0.105 - 0.157: 27 0.157 - 0.210: 0 0.210 - 0.262: 1 Chirality restraints: 767 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2 MAN B 4 " pdb=" C1 MAN B 4 " pdb=" C3 MAN B 4 " pdb=" O2 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.52 2.66 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL L 39 " pdb=" N VAL L 39 " pdb=" C VAL L 39 " pdb=" CB VAL L 39 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 764 not shown) Planarity restraints: 874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.001 2.00e-02 2.50e+03 1.61e-02 3.23e+00 pdb=" CG ASN A 329 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 126 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.005 2.00e-02 2.50e+03 9.49e-03 9.00e-01 pdb=" CG ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.006 2.00e-02 2.50e+03 ... (remaining 871 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 4308 3.21 - 3.77: 8010 3.77 - 4.34: 11814 4.34 - 4.90: 19472 Nonbonded interactions: 43711 Sorted by model distance: nonbonded pdb=" NE ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 2.080 3.120 nonbonded pdb=" OG SER A 331 " pdb=" O7 NAG A 503 " model vdw 2.147 3.040 nonbonded pdb=" OG SER A 219 " pdb=" OD2 ASP A 251 " model vdw 2.220 3.040 nonbonded pdb=" ND2 ASN H 56 " pdb=" O TYR A 284 " model vdw 2.252 3.120 nonbonded pdb=" O SER H 82B" pdb=" OG SER H 82B" model vdw 2.256 3.040 ... (remaining 43706 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.030 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.004 0.076 5027 Z= 0.196 Angle : 0.660 12.864 6856 Z= 0.324 Chirality : 0.046 0.262 767 Planarity : 0.003 0.040 870 Dihedral : 16.953 89.529 1739 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.85 % Allowed : 22.01 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.81 (0.34), residues: 616 helix: -0.15 (2.39), residues: 6 sheet: -0.23 (0.34), residues: 223 loop : -0.71 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 81 TYR 0.013 0.001 TYR A 121 PHE 0.011 0.002 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 5008) covalent geometry : angle 0.63940 / 0.32 ( 6810) SS BOND : bond 0.00334 / 0.20 ( 11) SS BOND : angle 1.81967 / 0.98 ( 22) hydrogen bonds : bond 0.21383 / 14.77 ( 160) hydrogen bonds : angle 9.31404 / 6.29 ( 441) link_ALPHA1-2 : bond 0.00465 / 0.24 ( 1) link_ALPHA1-2 : angle 1.68503 / 0.88 ( 3) link_ALPHA1-3 : bond 0.00181 / 0.10 ( 1) link_ALPHA1-3 : angle 1.56760 / 0.81 ( 3) link_BETA1-4 : bond 0.00316 / 0.16 ( 2) link_BETA1-4 : angle 1.87391 / 1.10 ( 6) link_NAG-ASN : bond 0.00152 / 0.08 ( 4) link_NAG-ASN : angle 2.72842 / 1.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.186 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 26 residues processed: 86 average time/residue: 0.3751 time to fit residues: 34.2570 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN A 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090093 restraints weight = 5758.407| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.24 r_work: 0.2948 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5027 Z= 0.127 Angle : 0.568 6.848 6856 Z= 0.300 Chirality : 0.046 0.251 767 Planarity : 0.004 0.043 870 Dihedral : 7.670 48.984 713 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.48 % Allowed : 20.15 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.71 (0.33), residues: 616 helix: -1.60 (1.72), residues: 7 sheet: 0.04 (0.34), residues: 216 loop : -0.74 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.017 0.001 TYR A 121 PHE 0.017 0.002 PHE A 132 TRP 0.011 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5008) covalent geometry : angle 0.56078 / 0.30 ( 6810) SS BOND : bond 0.00227 / 0.13 ( 11) SS BOND : angle 0.78701 / 0.67 ( 22) hydrogen bonds : bond 0.04334 / 3.15 ( 160) hydrogen bonds : angle 7.20839 / 4.88 ( 441) link_ALPHA1-2 : bond 0.00491 / 0.26 ( 1) link_ALPHA1-2 : angle 1.48125 / 0.77 ( 3) link_ALPHA1-3 : bond 0.00514 / 0.27 ( 1) link_ALPHA1-3 : angle 1.33942 / 0.72 ( 3) link_BETA1-4 : bond 0.00304 / 0.16 ( 2) link_BETA1-4 : angle 1.39454 / 0.86 ( 6) link_NAG-ASN : bond 0.00216 / 0.11 ( 4) link_NAG-ASN : angle 1.66459 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 430 ARG cc_start: 0.8344 (mmt90) cc_final: 0.8028 (mpt90) outliers start: 24 outliers final: 15 residues processed: 87 average time/residue: 0.3727 time to fit residues: 34.3078 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN L 27BASN A 131 GLN A 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.086156 restraints weight = 5784.503| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.23 r_work: 0.2886 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5027 Z= 0.237 Angle : 0.618 6.677 6856 Z= 0.324 Chirality : 0.047 0.178 767 Planarity : 0.004 0.045 870 Dihedral : 6.787 49.072 688 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.48 % Allowed : 20.90 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.85 (0.33), residues: 616 helix: -1.54 (1.69), residues: 7 sheet: -0.16 (0.33), residues: 222 loop : -0.77 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.017 0.002 TYR A 121 PHE 0.012 0.002 PHE A 354 TRP 0.014 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 ( 5008) covalent geometry : angle 0.60539 / 0.32 ( 6810) SS BOND : bond 0.00365 / 0.22 ( 11) SS BOND : angle 1.38998 / 1.30 ( 22) hydrogen bonds : bond 0.04351 / 3.15 ( 160) hydrogen bonds : angle 7.03400 / 4.78 ( 441) link_ALPHA1-2 : bond 0.00328 / 0.17 ( 1) link_ALPHA1-2 : angle 1.49760 / 0.80 ( 3) link_ALPHA1-3 : bond 0.00162 / 0.09 ( 1) link_ALPHA1-3 : angle 1.77718 / 0.95 ( 3) link_BETA1-4 : bond 0.00247 / 0.12 ( 2) link_BETA1-4 : angle 1.45793 / 0.90 ( 6) link_NAG-ASN : bond 0.00182 / 0.09 ( 4) link_NAG-ASN : angle 2.06807 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.192 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 82 average time/residue: 0.3731 time to fit residues: 32.3968 Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN A 91 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.088701 restraints weight = 5773.340| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.22 r_work: 0.2924 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5027 Z= 0.153 Angle : 0.580 6.716 6856 Z= 0.303 Chirality : 0.046 0.209 767 Planarity : 0.003 0.043 870 Dihedral : 6.473 52.573 686 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.85 % Allowed : 20.15 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.82 (0.33), residues: 616 helix: -1.58 (1.65), residues: 7 sheet: -0.17 (0.33), residues: 222 loop : -0.73 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.014 0.001 TYR A 121 PHE 0.012 0.002 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 5008) covalent geometry : angle 0.56401 / 0.30 ( 6810) SS BOND : bond 0.00312 / 0.18 ( 11) SS BOND : angle 1.37848 / 1.34 ( 22) hydrogen bonds : bond 0.03689 / 2.66 ( 160) hydrogen bonds : angle 6.76604 / 4.60 ( 441) link_ALPHA1-2 : bond 0.00396 / 0.21 ( 1) link_ALPHA1-2 : angle 1.43458 / 0.76 ( 3) link_ALPHA1-3 : bond 0.00508 / 0.27 ( 1) link_ALPHA1-3 : angle 1.49280 / 0.80 ( 3) link_BETA1-4 : bond 0.00288 / 0.14 ( 2) link_BETA1-4 : angle 1.44610 / 0.89 ( 6) link_NAG-ASN : bond 0.00088 / 0.05 ( 4) link_NAG-ASN : angle 2.42129 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.182 Fit side-chains REVERT: A 430 ARG cc_start: 0.8336 (mmt90) cc_final: 0.7850 (mmm160) outliers start: 26 outliers final: 18 residues processed: 86 average time/residue: 0.3483 time to fit residues: 31.6447 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN A 91 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.089867 restraints weight = 5841.822| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.25 r_work: 0.2945 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5027 Z= 0.132 Angle : 0.556 6.625 6856 Z= 0.290 Chirality : 0.046 0.253 767 Planarity : 0.003 0.042 870 Dihedral : 6.314 56.216 685 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.48 % Allowed : 21.64 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.80 (0.33), residues: 616 helix: -1.60 (1.61), residues: 7 sheet: -0.20 (0.33), residues: 227 loop : -0.69 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.013 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 5008) covalent geometry : angle 0.54347 / 0.29 ( 6810) SS BOND : bond 0.00197 / 0.12 ( 11) SS BOND : angle 0.91170 / 0.83 ( 22) hydrogen bonds : bond 0.03423 / 2.47 ( 160) hydrogen bonds : angle 6.56673 / 4.48 ( 441) link_ALPHA1-2 : bond 0.00380 / 0.20 ( 1) link_ALPHA1-2 : angle 1.41955 / 0.76 ( 3) link_ALPHA1-3 : bond 0.00436 / 0.23 ( 1) link_ALPHA1-3 : angle 1.44932 / 0.77 ( 3) link_BETA1-4 : bond 0.00350 / 0.17 ( 2) link_BETA1-4 : angle 1.43569 / 0.89 ( 6) link_NAG-ASN : bond 0.00116 / 0.06 ( 4) link_NAG-ASN : angle 2.36913 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 142 ASN cc_start: 0.7777 (t0) cc_final: 0.7552 (t160) REVERT: A 430 ARG cc_start: 0.8372 (mmt90) cc_final: 0.8113 (mpt90) outliers start: 24 outliers final: 15 residues processed: 87 average time/residue: 0.4345 time to fit residues: 39.7405 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN A 131 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.090820 restraints weight = 5863.999| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.24 r_work: 0.2957 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5027 Z= 0.126 Angle : 0.548 6.606 6856 Z= 0.284 Chirality : 0.046 0.239 767 Planarity : 0.003 0.042 870 Dihedral : 5.755 55.225 680 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.85 % Allowed : 21.64 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.72 (0.33), residues: 616 helix: -1.52 (1.64), residues: 7 sheet: -0.13 (0.33), residues: 222 loop : -0.64 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.013 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.011 0.001 TRP H 35A HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 5008) covalent geometry : angle 0.53632 / 0.28 ( 6810) SS BOND : bond 0.00205 / 0.12 ( 11) SS BOND : angle 0.70299 / 0.63 ( 22) hydrogen bonds : bond 0.03305 / 2.38 ( 160) hydrogen bonds : angle 6.43977 / 4.40 ( 441) link_ALPHA1-2 : bond 0.00397 / 0.21 ( 1) link_ALPHA1-2 : angle 1.42603 / 0.76 ( 3) link_ALPHA1-3 : bond 0.00514 / 0.27 ( 1) link_ALPHA1-3 : angle 1.47229 / 0.78 ( 3) link_BETA1-4 : bond 0.00337 / 0.17 ( 2) link_BETA1-4 : angle 1.41706 / 0.88 ( 6) link_NAG-ASN : bond 0.00161 / 0.08 ( 4) link_NAG-ASN : angle 2.27864 / 1.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 101 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8849 (m) REVERT: A 142 ASN cc_start: 0.7701 (t0) cc_final: 0.7386 (t160) REVERT: A 430 ARG cc_start: 0.8314 (mmt90) cc_final: 0.8085 (mpt90) outliers start: 26 outliers final: 20 residues processed: 91 average time/residue: 0.4131 time to fit residues: 39.6989 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN H 101 GLN A 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.087844 restraints weight = 5751.222| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.22 r_work: 0.2913 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5027 Z= 0.203 Angle : 0.592 6.646 6856 Z= 0.307 Chirality : 0.047 0.251 767 Planarity : 0.003 0.044 870 Dihedral : 5.876 54.854 680 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.04 % Allowed : 21.27 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.85 (0.33), residues: 616 helix: -1.48 (1.65), residues: 7 sheet: -0.19 (0.33), residues: 222 loop : -0.75 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.015 0.002 TYR A 121 PHE 0.014 0.002 PHE A 354 TRP 0.012 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 5008) covalent geometry : angle 0.57764 / 0.30 ( 6810) SS BOND : bond 0.00304 / 0.18 ( 11) SS BOND : angle 1.08747 / 0.90 ( 22) hydrogen bonds : bond 0.03623 / 2.60 ( 160) hydrogen bonds : angle 6.57071 / 4.49 ( 441) link_ALPHA1-2 : bond 0.00311 / 0.16 ( 1) link_ALPHA1-2 : angle 1.48792 / 0.79 ( 3) link_ALPHA1-3 : bond 0.00216 / 0.11 ( 1) link_ALPHA1-3 : angle 1.71639 / 0.91 ( 3) link_BETA1-4 : bond 0.00259 / 0.13 ( 2) link_BETA1-4 : angle 1.52187 / 0.94 ( 6) link_NAG-ASN : bond 0.00142 / 0.07 ( 4) link_NAG-ASN : angle 2.55621 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8433 (mtt180) cc_final: 0.8181 (mtt180) REVERT: A 91 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: A 142 ASN cc_start: 0.8033 (t0) cc_final: 0.7826 (t160) outliers start: 27 outliers final: 21 residues processed: 84 average time/residue: 0.3980 time to fit residues: 35.5473 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.089794 restraints weight = 5812.401| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.22 r_work: 0.2942 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5027 Z= 0.144 Angle : 0.560 6.595 6856 Z= 0.290 Chirality : 0.046 0.241 767 Planarity : 0.003 0.042 870 Dihedral : 5.698 50.965 680 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.48 % Allowed : 21.46 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.77 (0.33), residues: 616 helix: -1.29 (1.72), residues: 7 sheet: -0.19 (0.33), residues: 227 loop : -0.66 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.013 0.001 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5008) covalent geometry : angle 0.54812 / 0.29 ( 6810) SS BOND : bond 0.00194 / 0.12 ( 11) SS BOND : angle 0.82125 / 0.69 ( 22) hydrogen bonds : bond 0.03370 / 2.43 ( 160) hydrogen bonds : angle 6.46376 / 4.42 ( 441) link_ALPHA1-2 : bond 0.00354 / 0.19 ( 1) link_ALPHA1-2 : angle 1.43062 / 0.76 ( 3) link_ALPHA1-3 : bond 0.00453 / 0.24 ( 1) link_ALPHA1-3 : angle 1.50380 / 0.80 ( 3) link_BETA1-4 : bond 0.00311 / 0.16 ( 2) link_BETA1-4 : angle 1.47239 / 0.90 ( 6) link_NAG-ASN : bond 0.00136 / 0.07 ( 4) link_NAG-ASN : angle 2.32833 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8154 (mtt180) REVERT: A 91 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 101 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8841 (m) REVERT: A 142 ASN cc_start: 0.7731 (t0) cc_final: 0.7500 (t160) outliers start: 24 outliers final: 20 residues processed: 89 average time/residue: 0.3982 time to fit residues: 37.4852 Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 36 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091989 restraints weight = 5757.896| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.24 r_work: 0.2972 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5027 Z= 0.112 Angle : 0.540 6.529 6856 Z= 0.280 Chirality : 0.046 0.233 767 Planarity : 0.003 0.041 870 Dihedral : 5.407 39.680 680 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.29 % Allowed : 22.39 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.65 (0.33), residues: 616 helix: -1.21 (1.77), residues: 7 sheet: -0.08 (0.33), residues: 222 loop : -0.60 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.013 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.012 0.001 TRP H 35A HIS 0.001 0.000 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 5008) covalent geometry : angle 0.52974 / 0.28 ( 6810) SS BOND : bond 0.00160 / 0.10 ( 11) SS BOND : angle 0.65492 / 0.54 ( 22) hydrogen bonds : bond 0.03147 / 2.28 ( 160) hydrogen bonds : angle 6.31124 / 4.31 ( 441) link_ALPHA1-2 : bond 0.00413 / 0.22 ( 1) link_ALPHA1-2 : angle 1.40944 / 0.75 ( 3) link_ALPHA1-3 : bond 0.00567 / 0.30 ( 1) link_ALPHA1-3 : angle 1.41598 / 0.75 ( 3) link_BETA1-4 : bond 0.00380 / 0.19 ( 2) link_BETA1-4 : angle 1.40239 / 0.86 ( 6) link_NAG-ASN : bond 0.00164 / 0.08 ( 4) link_NAG-ASN : angle 2.11265 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8137 (mtt180) REVERT: A 140 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8720 (tp) outliers start: 23 outliers final: 20 residues processed: 86 average time/residue: 0.4338 time to fit residues: 39.2077 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN H 101 GLN A 131 GLN A 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086628 restraints weight = 5806.814| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.21 r_work: 0.2896 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5027 Z= 0.251 Angle : 0.625 6.627 6856 Z= 0.325 Chirality : 0.048 0.259 767 Planarity : 0.004 0.045 870 Dihedral : 5.661 42.108 680 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.10 % Allowed : 23.13 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.81 (0.33), residues: 616 helix: -1.14 (1.76), residues: 7 sheet: -0.18 (0.33), residues: 222 loop : -0.72 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 81 TYR 0.017 0.002 TYR A 121 PHE 0.014 0.002 PHE A 354 TRP 0.017 0.002 TRP H 47 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 ( 5008) covalent geometry : angle 0.61049 / 0.32 ( 6810) SS BOND : bond 0.00344 / 0.23 ( 11) SS BOND : angle 1.03935 / 0.88 ( 22) hydrogen bonds : bond 0.03783 / 2.72 ( 160) hydrogen bonds : angle 6.59012 / 4.50 ( 441) link_ALPHA1-2 : bond 0.00283 / 0.15 ( 1) link_ALPHA1-2 : angle 1.51787 / 0.80 ( 3) link_ALPHA1-3 : bond 0.00015 / 0.01 ( 1) link_ALPHA1-3 : angle 1.82569 / 0.97 ( 3) link_BETA1-4 : bond 0.00163 / 0.08 ( 2) link_BETA1-4 : angle 1.57611 / 0.97 ( 6) link_NAG-ASN : bond 0.00212 / 0.11 ( 4) link_NAG-ASN : angle 2.64706 / 1.75 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: H 82 SER cc_start: 0.8276 (t) cc_final: 0.7886 (p) REVERT: A 85 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8168 (mtt180) REVERT: A 140 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8614 (tp) outliers start: 22 outliers final: 19 residues processed: 80 average time/residue: 0.3833 time to fit residues: 32.5002 Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.089962 restraints weight = 5811.166| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.20 r_work: 0.2947 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5027 Z= 0.142 Angle : 0.565 6.575 6856 Z= 0.294 Chirality : 0.046 0.237 767 Planarity : 0.003 0.042 870 Dihedral : 5.488 38.813 680 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.54 % Allowed : 24.25 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.71 (0.33), residues: 616 helix: -1.11 (1.81), residues: 7 sheet: -0.17 (0.33), residues: 227 loop : -0.61 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 400 TYR 0.014 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 5008) covalent geometry : angle 0.55397 / 0.29 ( 6810) SS BOND : bond 0.00198 / 0.13 ( 11) SS BOND : angle 0.73941 / 0.63 ( 22) hydrogen bonds : bond 0.03338 / 2.42 ( 160) hydrogen bonds : angle 6.42721 / 4.38 ( 441) link_ALPHA1-2 : bond 0.00362 / 0.19 ( 1) link_ALPHA1-2 : angle 1.43507 / 0.76 ( 3) link_ALPHA1-3 : bond 0.00448 / 0.24 ( 1) link_ALPHA1-3 : angle 1.46640 / 0.79 ( 3) link_BETA1-4 : bond 0.00330 / 0.16 ( 2) link_BETA1-4 : angle 1.49259 / 0.91 ( 6) link_NAG-ASN : bond 0.00134 / 0.07 ( 4) link_NAG-ASN : angle 2.26945 / 1.50 ( 12) =============================================================================== Job complete usr+sys time: 2220.63 seconds wall clock time: 38 minutes 39.41 seconds (2319.41 seconds total)