Starting phenix.real_space_refine on Tue Mar 3 17:41:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6y_31753/03_2026/7v6y_31753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6y_31753/03_2026/7v6y_31753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v6y_31753/03_2026/7v6y_31753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6y_31753/03_2026/7v6y_31753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6y_31753/03_2026/7v6y_31753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6y_31753/03_2026/7v6y_31753.map" } resolution = 3.5 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 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= 0.002 sd= 0.075 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 C 4923 2.51 5 N 1221 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7484 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7326 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 44, 'TRANS': 945} Chain breaks: 2 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 23, 'GLN:plan1': 5, 'TYR:plan': 2, 'ASP:plan': 29, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 343 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 130 Unusual residues: {'5VI': 1, 'CLR': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.66, per 1000 atoms: 0.22 Number of scatterers: 7484 At special positions: 0 Unit cell: (93.48, 86.92, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 1 15.00 O 1301 8.00 N 1221 7.00 C 4923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1204 " - " ASN A 127 " " NAG A1206 " - " ASN A 400 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 310.6 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 64.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 61 through 83 removed outlier: 3.661A pdb=" N LEU A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 101 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 157 through 173 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 202 through 209 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.572A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TRP A 222 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU A 223 " --> pdb=" O CYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.587A pdb=" N PHE A 245 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 294 through 298 removed outlier: 4.141A pdb=" N ASN A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.612A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.754A pdb=" N GLY A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.786A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 397 removed outlier: 4.529A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 455 through 478 removed outlier: 3.768A pdb=" N LEU A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 514 Proline residue: A 490 - end of helix removed outlier: 4.007A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 549 removed outlier: 3.624A pdb=" N GLU A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 575 Processing helix chain 'A' and resid 576 through 592 removed outlier: 4.071A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.544A pdb=" N ALA A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 732 through 756 removed outlier: 4.066A pdb=" N VAL A 738 " --> pdb=" O LYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.931A pdb=" N HIS A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 810 " --> pdb=" O TYR A 806 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 852 Processing helix chain 'A' and resid 865 through 875 removed outlier: 3.594A pdb=" N GLN A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.795A pdb=" N TYR A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 991 removed outlier: 3.573A pdb=" N LEU A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.512A pdb=" N TRP A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1034 Processing helix chain 'A' and resid 1035 through 1061 Processing helix chain 'A' and resid 1065 through 1093 removed outlier: 4.566A pdb=" N HIS A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1127 removed outlier: 3.747A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Proline residue: A1111 - end of helix Processing helix chain 'A' and resid 1131 through 1164 removed outlier: 3.547A pdb=" N VAL A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A1139 " --> pdb=" O VAL A1135 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.538A pdb=" N CYS A 313 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 4.043A pdb=" N SER A 342 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA5, first strand: chain 'A' and resid 963 through 965 465 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1135 1.28 - 1.41: 2003 1.41 - 1.54: 4444 1.54 - 1.68: 32 1.68 - 1.81: 60 Bond restraints: 7674 Sorted by residual: bond pdb=" C LEU A1145 " pdb=" O LEU A1145 " ideal model delta sigma weight residual 1.237 1.146 0.090 1.17e-02 7.31e+03 5.98e+01 bond pdb=" CA HIS A 164 " pdb=" C HIS A 164 " ideal model delta sigma weight residual 1.523 1.425 0.099 1.30e-02 5.92e+03 5.77e+01 bond pdb=" CA ALA A 921 " pdb=" C ALA A 921 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.29e-02 6.01e+03 4.92e+01 bond pdb=" CA GLN A 228 " pdb=" C GLN A 228 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.24e-02 6.50e+03 4.92e+01 bond pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.29e-02 6.01e+03 4.31e+01 ... (remaining 7669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 9410 2.78 - 5.55: 889 5.55 - 8.33: 144 8.33 - 11.10: 56 11.10 - 13.88: 13 Bond angle restraints: 10512 Sorted by residual: angle pdb=" N THR A 293 " pdb=" CA THR A 293 " pdb=" C THR A 293 " ideal model delta sigma weight residual 113.17 99.29 13.88 1.26e+00 6.30e-01 1.21e+02 angle pdb=" N LYS A 339 " pdb=" CA LYS A 339 " pdb=" C LYS A 339 " ideal model delta sigma weight residual 111.28 122.74 -11.46 1.09e+00 8.42e-01 1.10e+02 angle pdb=" N GLN A 794 " pdb=" CA GLN A 794 " pdb=" C GLN A 794 " ideal model delta sigma weight residual 111.14 122.39 -11.25 1.08e+00 8.57e-01 1.09e+02 angle pdb=" N THR A 764 " pdb=" CA THR A 764 " pdb=" C THR A 764 " ideal model delta sigma weight residual 113.23 101.13 12.10 1.24e+00 6.50e-01 9.53e+01 angle pdb=" N ILE A 328 " pdb=" CA ILE A 328 " pdb=" C ILE A 328 " ideal model delta sigma weight residual 111.67 120.48 -8.81 9.50e-01 1.11e+00 8.61e+01 ... (remaining 10507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4070 16.95 - 33.90: 380 33.90 - 50.86: 138 50.86 - 67.81: 46 67.81 - 84.76: 11 Dihedral angle restraints: 4645 sinusoidal: 1758 harmonic: 2887 Sorted by residual: dihedral pdb=" CB CYS A 282 " pdb=" SG CYS A 282 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual 93.00 171.16 -78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" C PHE A1131 " pdb=" N PHE A1131 " pdb=" CA PHE A1131 " pdb=" CB PHE A1131 " ideal model delta harmonic sigma weight residual -122.60 -138.95 16.35 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" N PHE A1131 " pdb=" C PHE A1131 " pdb=" CA PHE A1131 " pdb=" CB PHE A1131 " ideal model delta harmonic sigma weight residual 122.80 138.50 -15.70 0 2.50e+00 1.60e-01 3.95e+01 ... (remaining 4642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 977 0.139 - 0.278: 234 0.278 - 0.418: 39 0.418 - 0.557: 11 0.557 - 0.696: 4 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA PHE A 743 " pdb=" N PHE A 743 " pdb=" C PHE A 743 " pdb=" CB PHE A 743 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA PHE A1131 " pdb=" N PHE A1131 " pdb=" C PHE A1131 " pdb=" CB PHE A1131 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP A 183 " pdb=" N TRP A 183 " pdb=" C TRP A 183 " pdb=" CB TRP A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.50e+00 ... (remaining 1262 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.199 2.00e-02 2.50e+03 1.64e-01 3.36e+02 pdb=" C7 NAG B 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.266 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1157 " -0.086 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO A1158 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 361 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C HIS A 361 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS A 361 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE A 362 " 0.030 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2189 2.79 - 3.31: 7486 3.31 - 3.84: 12182 3.84 - 4.37: 14405 4.37 - 4.90: 23391 Nonbonded interactions: 59653 Sorted by model distance: nonbonded pdb=" OE2 GLU A 108 " pdb=" CB SER A 480 " model vdw 2.258 3.440 nonbonded pdb=" O SER A 401 " pdb=" OG1 THR A 402 " model vdw 2.269 3.040 nonbonded pdb=" N THR A 293 " pdb=" N ALA A 294 " model vdw 2.281 2.560 nonbonded pdb=" O PHE A 545 " pdb=" OG SER A 560 " model vdw 2.339 3.040 nonbonded pdb=" N MET A 178 " pdb=" O MET A 178 " model vdw 2.342 2.496 ... (remaining 59648 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: 1.230 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.350 Find NCS groups from input model: 0.040 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.014 0.099 7680 Z= 1.028 Angle : 1.856 13.878 10527 Z= 1.262 Chirality : 0.132 0.696 1265 Planarity : 0.012 0.164 1295 Dihedral : 16.465 84.758 2776 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.51 % Rotamer: Outliers : 11.06 % Allowed : 11.91 % Favored : 77.02 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.26), residues: 984 helix: 1.40 (0.21), residues: 589 sheet: 0.32 (0.72), residues: 49 loop : -1.38 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1100 TYR 0.028 0.003 TYR A 920 PHE 0.034 0.003 PHE A1133 TRP 0.020 0.002 TRP A 830 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.01393 ( 7674) covalent geometry : angle 1.85493 (10512) SS BOND : bond 0.00806 ( 3) SS BOND : angle 1.66413 ( 6) hydrogen bonds : bond 0.19619 ( 465) hydrogen bonds : angle 7.44394 ( 1362) link_BETA1-4 : bond 0.00779 ( 1) link_BETA1-4 : angle 2.45176 ( 3) link_NAG-ASN : bond 0.00462 ( 2) link_NAG-ASN : angle 3.29661 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 0.286 Fit side-chains REVERT: A 115 TRP cc_start: 0.5942 (OUTLIER) cc_final: 0.5167 (t60) REVERT: A 181 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6548 (mmm160) REVERT: A 182 GLN cc_start: 0.7559 (tp40) cc_final: 0.7112 (tp-100) REVERT: A 259 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6680 (t80) REVERT: A 264 TRP cc_start: 0.6988 (m-90) cc_final: 0.6526 (m-90) REVERT: A 349 MET cc_start: 0.7665 (mtt) cc_final: 0.7413 (mtt) REVERT: A 358 MET cc_start: 0.8183 (ttt) cc_final: 0.7900 (ttt) REVERT: A 367 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.6054 (t80) REVERT: A 444 LEU cc_start: 0.7921 (tp) cc_final: 0.7611 (mp) REVERT: A 479 ILE cc_start: 0.9160 (mt) cc_final: 0.8951 (mt) REVERT: A 588 ARG cc_start: 0.7675 (tmm-80) cc_final: 0.6669 (mmt-90) REVERT: A 794 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7186 (mt0) REVERT: A 1134 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7653 (mp) outliers start: 78 outliers final: 19 residues processed: 226 average time/residue: 0.0881 time to fit residues: 27.1742 Evaluate side-chains 153 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 182 GLN A 244 ASN A 269 ASN A 284 ASN A 344 HIS A 351 GLN A 506 HIS A 570 ASN A 780 GLN A 800 ASN A 809 HIS A 891 GLN A 901 ASN A 985 ASN A1085 HIS ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.225153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.179438 restraints weight = 7563.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.182386 restraints weight = 6342.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.184765 restraints weight = 4163.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.184801 restraints weight = 3242.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.185237 restraints weight = 3132.388| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7680 Z= 0.172 Angle : 0.716 9.237 10527 Z= 0.368 Chirality : 0.044 0.180 1265 Planarity : 0.006 0.072 1295 Dihedral : 10.779 58.679 1375 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.82 % Allowed : 17.30 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.26), residues: 984 helix: 1.32 (0.20), residues: 606 sheet: 0.30 (0.73), residues: 48 loop : -1.54 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 892 TYR 0.022 0.002 TYR A 190 PHE 0.034 0.002 PHE A1133 TRP 0.022 0.002 TRP A 373 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7674) covalent geometry : angle 0.71210 (10512) SS BOND : bond 0.00108 ( 3) SS BOND : angle 1.78889 ( 6) hydrogen bonds : bond 0.05973 ( 465) hydrogen bonds : angle 5.04755 ( 1362) link_BETA1-4 : bond 0.00255 ( 1) link_BETA1-4 : angle 2.94230 ( 3) link_NAG-ASN : bond 0.00202 ( 2) link_NAG-ASN : angle 1.97932 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.302 Fit side-chains REVERT: A 259 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.5617 (t80) REVERT: A 349 MET cc_start: 0.7612 (mtt) cc_final: 0.7392 (mtt) REVERT: A 373 TRP cc_start: 0.6238 (t-100) cc_final: 0.5956 (t-100) REVERT: A 479 ILE cc_start: 0.9175 (mt) cc_final: 0.8888 (mt) REVERT: A 519 PHE cc_start: 0.7432 (t80) cc_final: 0.7118 (t80) REVERT: A 588 ARG cc_start: 0.7575 (tmm-80) cc_final: 0.6924 (mpt180) REVERT: A 797 ASP cc_start: 0.7449 (p0) cc_final: 0.6993 (p0) REVERT: A 841 LEU cc_start: 0.8190 (mt) cc_final: 0.7719 (mp) REVERT: A 901 ASN cc_start: 0.8347 (t0) cc_final: 0.8093 (t0) REVERT: A 949 ILE cc_start: 0.7266 (mm) cc_final: 0.6984 (mm) REVERT: A 1134 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7797 (mp) outliers start: 41 outliers final: 21 residues processed: 167 average time/residue: 0.0775 time to fit residues: 18.4044 Evaluate side-chains 138 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 344 HIS A 506 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.226202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.181295 restraints weight = 7475.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.183874 restraints weight = 6730.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.186550 restraints weight = 4498.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186261 restraints weight = 3464.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.186510 restraints weight = 3278.601| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7680 Z= 0.154 Angle : 0.635 7.526 10527 Z= 0.327 Chirality : 0.042 0.175 1265 Planarity : 0.006 0.057 1295 Dihedral : 8.672 59.900 1342 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.39 % Allowed : 18.16 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.26), residues: 984 helix: 1.38 (0.20), residues: 602 sheet: 0.25 (0.71), residues: 48 loop : -1.39 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1136 TYR 0.027 0.002 TYR A 190 PHE 0.029 0.002 PHE A1133 TRP 0.019 0.002 TRP A 64 HIS 0.011 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7674) covalent geometry : angle 0.63064 (10512) SS BOND : bond 0.00064 ( 3) SS BOND : angle 1.72981 ( 6) hydrogen bonds : bond 0.05312 ( 465) hydrogen bonds : angle 4.85329 ( 1362) link_BETA1-4 : bond 0.00249 ( 1) link_BETA1-4 : angle 2.68823 ( 3) link_NAG-ASN : bond 0.00181 ( 2) link_NAG-ASN : angle 1.78217 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.283 Fit side-chains REVERT: A 259 TYR cc_start: 0.6393 (OUTLIER) cc_final: 0.5147 (t80) REVERT: A 349 MET cc_start: 0.7935 (mtt) cc_final: 0.7685 (mtt) REVERT: A 479 ILE cc_start: 0.9191 (mt) cc_final: 0.8925 (mt) REVERT: A 494 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6480 (tp) REVERT: A 588 ARG cc_start: 0.7599 (tmm-80) cc_final: 0.6880 (mmt-90) REVERT: A 797 ASP cc_start: 0.7249 (p0) cc_final: 0.6988 (p0) REVERT: A 1134 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7905 (mp) outliers start: 38 outliers final: 24 residues processed: 156 average time/residue: 0.0821 time to fit residues: 17.8318 Evaluate side-chains 137 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 96 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.227147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.183026 restraints weight = 7609.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.182138 restraints weight = 8096.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.185200 restraints weight = 5887.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185673 restraints weight = 4514.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.187026 restraints weight = 3889.270| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7680 Z= 0.137 Angle : 0.607 8.094 10527 Z= 0.309 Chirality : 0.042 0.187 1265 Planarity : 0.005 0.052 1295 Dihedral : 7.840 57.278 1342 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.39 % Allowed : 20.00 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.69 (0.26), residues: 984 helix: 1.51 (0.21), residues: 598 sheet: 0.31 (0.73), residues: 48 loop : -1.47 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 892 TYR 0.025 0.001 TYR A 190 PHE 0.025 0.002 PHE A1133 TRP 0.026 0.002 TRP A 64 HIS 0.007 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7674) covalent geometry : angle 0.60439 (10512) SS BOND : bond 0.00131 ( 3) SS BOND : angle 1.17925 ( 6) hydrogen bonds : bond 0.04707 ( 465) hydrogen bonds : angle 4.62183 ( 1362) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 2.55632 ( 3) link_NAG-ASN : bond 0.00183 ( 2) link_NAG-ASN : angle 1.64450 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7831 (t80) cc_final: 0.7609 (t80) REVERT: A 231 THR cc_start: 0.8666 (t) cc_final: 0.8385 (p) REVERT: A 259 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.4756 (t80) REVERT: A 314 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7727 (pt0) REVERT: A 349 MET cc_start: 0.7929 (mtt) cc_final: 0.7678 (mtt) REVERT: A 450 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7838 (ptpp) REVERT: A 479 ILE cc_start: 0.9171 (mt) cc_final: 0.8913 (mt) REVERT: A 588 ARG cc_start: 0.7518 (tmm-80) cc_final: 0.6919 (mpt180) REVERT: A 797 ASP cc_start: 0.7246 (p0) cc_final: 0.6959 (p0) REVERT: A 1134 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7716 (mt) outliers start: 38 outliers final: 25 residues processed: 155 average time/residue: 0.0752 time to fit residues: 16.5375 Evaluate side-chains 142 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.222073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179150 restraints weight = 7565.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177923 restraints weight = 8318.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184327 restraints weight = 5979.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183919 restraints weight = 3493.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.184137 restraints weight = 3259.090| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7680 Z= 0.137 Angle : 0.604 8.459 10527 Z= 0.302 Chirality : 0.041 0.186 1265 Planarity : 0.005 0.057 1295 Dihedral : 7.328 56.638 1342 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.25 % Allowed : 23.40 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.26), residues: 984 helix: 1.52 (0.20), residues: 602 sheet: 0.27 (0.77), residues: 48 loop : -1.47 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 892 TYR 0.020 0.001 TYR A 190 PHE 0.023 0.001 PHE A1133 TRP 0.017 0.001 TRP A 64 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7674) covalent geometry : angle 0.60077 (10512) SS BOND : bond 0.00377 ( 3) SS BOND : angle 1.48604 ( 6) hydrogen bonds : bond 0.04652 ( 465) hydrogen bonds : angle 4.57866 ( 1362) link_BETA1-4 : bond 0.00009 ( 1) link_BETA1-4 : angle 2.43288 ( 3) link_NAG-ASN : bond 0.00184 ( 2) link_NAG-ASN : angle 1.59777 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7681 (t80) cc_final: 0.7414 (t80) REVERT: A 259 TYR cc_start: 0.6211 (OUTLIER) cc_final: 0.4751 (t80) REVERT: A 349 MET cc_start: 0.8044 (mtt) cc_final: 0.7708 (mtp) REVERT: A 403 GLN cc_start: 0.6913 (mm110) cc_final: 0.6650 (mm110) REVERT: A 479 ILE cc_start: 0.9194 (mt) cc_final: 0.8925 (mt) REVERT: A 494 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.6028 (tp) REVERT: A 588 ARG cc_start: 0.7611 (tmm-80) cc_final: 0.6901 (mpt180) REVERT: A 797 ASP cc_start: 0.7231 (p0) cc_final: 0.6945 (p0) REVERT: A 1134 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7720 (mt) outliers start: 37 outliers final: 23 residues processed: 139 average time/residue: 0.0714 time to fit residues: 14.2413 Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.225345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.183311 restraints weight = 7532.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.182731 restraints weight = 7691.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.185995 restraints weight = 6504.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185864 restraints weight = 4342.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.187043 restraints weight = 3639.593| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7680 Z= 0.121 Angle : 0.573 8.428 10527 Z= 0.288 Chirality : 0.040 0.198 1265 Planarity : 0.005 0.058 1295 Dihedral : 6.938 58.049 1341 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.83 % Allowed : 24.54 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.27), residues: 984 helix: 1.71 (0.21), residues: 599 sheet: 0.23 (0.79), residues: 48 loop : -1.50 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 892 TYR 0.029 0.001 TYR A 190 PHE 0.019 0.001 PHE A1133 TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7674) covalent geometry : angle 0.57038 (10512) SS BOND : bond 0.00032 ( 3) SS BOND : angle 1.10513 ( 6) hydrogen bonds : bond 0.04239 ( 465) hydrogen bonds : angle 4.43979 ( 1362) link_BETA1-4 : bond 0.00147 ( 1) link_BETA1-4 : angle 2.31362 ( 3) link_NAG-ASN : bond 0.00204 ( 2) link_NAG-ASN : angle 1.46882 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7635 (t80) cc_final: 0.7325 (t80) REVERT: A 259 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.4720 (t80) REVERT: A 349 MET cc_start: 0.8041 (mtt) cc_final: 0.7736 (mtp) REVERT: A 479 ILE cc_start: 0.9176 (mt) cc_final: 0.8949 (mt) REVERT: A 588 ARG cc_start: 0.7569 (tmm-80) cc_final: 0.6912 (mpt180) REVERT: A 949 ILE cc_start: 0.6441 (mm) cc_final: 0.6149 (mm) REVERT: A 1134 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7739 (mt) outliers start: 27 outliers final: 20 residues processed: 130 average time/residue: 0.0806 time to fit residues: 14.7660 Evaluate side-chains 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 89 optimal weight: 0.2980 chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 GLN A 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.221612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.176912 restraints weight = 7590.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176257 restraints weight = 8070.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180727 restraints weight = 5930.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180421 restraints weight = 4210.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.180644 restraints weight = 3601.371| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7680 Z= 0.167 Angle : 0.633 11.143 10527 Z= 0.318 Chirality : 0.042 0.180 1265 Planarity : 0.005 0.056 1295 Dihedral : 7.012 58.106 1341 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.11 % Allowed : 24.54 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.73 (0.26), residues: 984 helix: 1.54 (0.20), residues: 604 sheet: 0.03 (0.79), residues: 48 loop : -1.46 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 892 TYR 0.025 0.002 TYR A 190 PHE 0.025 0.002 PHE A1133 TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7674) covalent geometry : angle 0.63085 (10512) SS BOND : bond 0.00211 ( 3) SS BOND : angle 1.35323 ( 6) hydrogen bonds : bond 0.04959 ( 465) hydrogen bonds : angle 4.57960 ( 1362) link_BETA1-4 : bond 0.00042 ( 1) link_BETA1-4 : angle 2.29185 ( 3) link_NAG-ASN : bond 0.00213 ( 2) link_NAG-ASN : angle 1.41134 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7690 (t80) cc_final: 0.7339 (t80) REVERT: A 259 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.4609 (t80) REVERT: A 349 MET cc_start: 0.8060 (mtt) cc_final: 0.7741 (mtp) REVERT: A 479 ILE cc_start: 0.9199 (mt) cc_final: 0.8980 (mt) REVERT: A 588 ARG cc_start: 0.7659 (tmm-80) cc_final: 0.6972 (mpt180) REVERT: A 1134 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7734 (mt) outliers start: 36 outliers final: 20 residues processed: 142 average time/residue: 0.0759 time to fit residues: 15.2992 Evaluate side-chains 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 45 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.227369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182988 restraints weight = 7608.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.181799 restraints weight = 8479.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186068 restraints weight = 6444.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.185838 restraints weight = 4543.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186617 restraints weight = 3997.716| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7680 Z= 0.129 Angle : 0.601 10.471 10527 Z= 0.301 Chirality : 0.040 0.160 1265 Planarity : 0.005 0.057 1295 Dihedral : 6.736 59.047 1341 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.11 % Allowed : 25.53 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.87 (0.27), residues: 984 helix: 1.69 (0.21), residues: 604 sheet: 0.04 (0.81), residues: 48 loop : -1.50 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 892 TYR 0.027 0.001 TYR A 190 PHE 0.019 0.001 PHE A1133 TRP 0.013 0.001 TRP A 373 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7674) covalent geometry : angle 0.59717 (10512) SS BOND : bond 0.00131 ( 3) SS BOND : angle 2.16847 ( 6) hydrogen bonds : bond 0.04327 ( 465) hydrogen bonds : angle 4.43694 ( 1362) link_BETA1-4 : bond 0.00175 ( 1) link_BETA1-4 : angle 2.21468 ( 3) link_NAG-ASN : bond 0.00210 ( 2) link_NAG-ASN : angle 1.37796 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7630 (t80) cc_final: 0.7320 (t80) REVERT: A 259 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.4442 (t80) REVERT: A 349 MET cc_start: 0.8064 (mtt) cc_final: 0.7764 (mtp) REVERT: A 479 ILE cc_start: 0.9215 (mt) cc_final: 0.8987 (mt) REVERT: A 547 MET cc_start: 0.7252 (tpp) cc_final: 0.6952 (mmt) REVERT: A 585 ASP cc_start: 0.7794 (t0) cc_final: 0.7416 (t0) REVERT: A 588 ARG cc_start: 0.7643 (tmm-80) cc_final: 0.6907 (mpt180) REVERT: A 1134 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7803 (mt) outliers start: 29 outliers final: 17 residues processed: 137 average time/residue: 0.0722 time to fit residues: 14.1829 Evaluate side-chains 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.221014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176995 restraints weight = 7531.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.175968 restraints weight = 8113.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.181767 restraints weight = 6064.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.181119 restraints weight = 4041.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.181436 restraints weight = 3321.710| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7680 Z= 0.152 Angle : 0.628 11.604 10527 Z= 0.312 Chirality : 0.041 0.160 1265 Planarity : 0.005 0.056 1295 Dihedral : 6.816 59.890 1341 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.84 % Allowed : 26.38 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.74 (0.27), residues: 984 helix: 1.59 (0.20), residues: 606 sheet: -0.00 (0.81), residues: 48 loop : -1.56 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 892 TYR 0.025 0.001 TYR A 190 PHE 0.023 0.002 PHE A 786 TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7674) covalent geometry : angle 0.62460 (10512) SS BOND : bond 0.00141 ( 3) SS BOND : angle 2.03943 ( 6) hydrogen bonds : bond 0.04711 ( 465) hydrogen bonds : angle 4.51882 ( 1362) link_BETA1-4 : bond 0.00097 ( 1) link_BETA1-4 : angle 2.14522 ( 3) link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 1.30551 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7627 (t80) cc_final: 0.7322 (t80) REVERT: A 259 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.4370 (t80) REVERT: A 349 MET cc_start: 0.8058 (mtt) cc_final: 0.7738 (mtp) REVERT: A 479 ILE cc_start: 0.9217 (mt) cc_final: 0.8983 (mt) REVERT: A 547 MET cc_start: 0.7283 (tpp) cc_final: 0.6928 (mmt) REVERT: A 585 ASP cc_start: 0.7823 (t0) cc_final: 0.7439 (t0) REVERT: A 588 ARG cc_start: 0.7688 (tmm-80) cc_final: 0.6964 (mpt180) REVERT: A 1134 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7793 (mt) outliers start: 20 outliers final: 17 residues processed: 128 average time/residue: 0.0713 time to fit residues: 12.9701 Evaluate side-chains 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 73 optimal weight: 0.0050 chunk 32 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 244 ASN A 800 ASN ** A 915 ASN ** 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 = 0.4472 r_free = 0.4472 target = 0.228843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185215 restraints weight = 7534.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.184522 restraints weight = 8065.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190376 restraints weight = 5905.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189158 restraints weight = 4169.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189580 restraints weight = 3626.819| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7680 Z= 0.124 Angle : 0.603 10.968 10527 Z= 0.300 Chirality : 0.040 0.157 1265 Planarity : 0.005 0.058 1295 Dihedral : 6.541 57.062 1340 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.84 % Allowed : 27.23 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.27), residues: 984 helix: 1.70 (0.21), residues: 606 sheet: 0.06 (0.82), residues: 48 loop : -1.54 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 892 TYR 0.024 0.001 TYR A 190 PHE 0.018 0.001 PHE A1133 TRP 0.021 0.001 TRP A 830 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7674) covalent geometry : angle 0.60092 (10512) SS BOND : bond 0.00054 ( 3) SS BOND : angle 1.36967 ( 6) hydrogen bonds : bond 0.04147 ( 465) hydrogen bonds : angle 4.41492 ( 1362) link_BETA1-4 : bond 0.00091 ( 1) link_BETA1-4 : angle 2.08276 ( 3) link_NAG-ASN : bond 0.00200 ( 2) link_NAG-ASN : angle 1.27611 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7553 (t80) cc_final: 0.7287 (t80) REVERT: A 259 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.4172 (t80) REVERT: A 349 MET cc_start: 0.8077 (mtt) cc_final: 0.7777 (mtp) REVERT: A 433 LEU cc_start: 0.7563 (tt) cc_final: 0.6715 (mp) REVERT: A 479 ILE cc_start: 0.9190 (mt) cc_final: 0.8973 (mt) REVERT: A 585 ASP cc_start: 0.7766 (t0) cc_final: 0.7395 (t0) REVERT: A 588 ARG cc_start: 0.7646 (tmm-80) cc_final: 0.6936 (mpt180) REVERT: A 1134 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7828 (mt) REVERT: A 1142 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7321 (mt) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 0.0728 time to fit residues: 13.4662 Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1131 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 0.0060 chunk 23 optimal weight: 0.0010 chunk 89 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.231509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.187509 restraints weight = 7510.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.186422 restraints weight = 8074.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190531 restraints weight = 6701.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.190461 restraints weight = 4238.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.191152 restraints weight = 3822.744| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7680 Z= 0.119 Angle : 0.588 9.769 10527 Z= 0.294 Chirality : 0.040 0.157 1265 Planarity : 0.005 0.059 1295 Dihedral : 6.363 54.175 1340 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.41 % Allowed : 27.38 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.27), residues: 984 helix: 1.80 (0.21), residues: 606 sheet: 0.10 (0.81), residues: 48 loop : -1.45 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 892 TYR 0.024 0.001 TYR A 190 PHE 0.026 0.001 PHE A 786 TRP 0.018 0.001 TRP A 934 HIS 0.004 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7674) covalent geometry : angle 0.58632 (10512) SS BOND : bond 0.00049 ( 3) SS BOND : angle 1.26960 ( 6) hydrogen bonds : bond 0.03970 ( 465) hydrogen bonds : angle 4.35367 ( 1362) link_BETA1-4 : bond 0.00132 ( 1) link_BETA1-4 : angle 1.97763 ( 3) link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 1.17885 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.21 seconds wall clock time: 24 minutes 34.48 seconds (1474.48 seconds total)