Starting phenix.real_space_refine on Thu Jul 2 07:48:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v6y_31753/07_2026/7v6y_31753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6y_31753/07_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_31753/07_2026/7v6y_31753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6y_31753/07_2026/7v6y_31753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6y_31753/07_2026/7v6y_31753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6y_31753/07_2026/7v6y_31753.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v6y_31753/07_2026/7v6y_31753.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v6y_31753/07_2026/7v6y_31753.cif" } 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-6108/lib/python3.11/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 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 chiralities: 3 Time building chain proxies: 1.57, per 1000 atoms: 0.21 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: 0.66 Conformation dependent library (CDL) restraints added in 482.7 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: 0.17 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: 1.23 Time building geometry restraints manager: 0.91 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: 3907 16.95 - 33.90: 348 33.90 - 50.86: 124 50.86 - 67.81: 40 67.81 - 84.76: 9 Dihedral angle restraints: 4428 sinusoidal: 1541 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 4425 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: 0.010 Normalize map: mean=0, sd=1: 1.190 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.260 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 16.196 84.758 2559 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/Z covalent geometry : bond 0.01393 / 1.03 ( 7674) covalent geometry : angle 1.85493 / 1.26 (10512) SS BOND : bond 0.00806 / 0.42 ( 3) SS BOND : angle 1.66413 / 0.93 ( 6) hydrogen bonds : bond 0.19619 / 13.11 ( 465) hydrogen bonds : angle 7.44394 / 5.29 ( 1362) link_BETA1-4 : bond 0.00779 / 0.41 ( 1) link_BETA1-4 : angle 2.45176 / 1.38 ( 3) link_NAG-ASN : bond 0.00462 / 0.24 ( 2) link_NAG-ASN : angle 3.29661 / 1.35 ( 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 : 0.342 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: 0.0856 time to fit residues: 26.6163 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 : 0.273 ------------------------------------------------------------------------------- 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... A 142 GLN A 182 GLN A 244 ASN A 269 ASN A 284 ASN A 296 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 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 = 0.4422 r_free = 0.4422 target = 0.224687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178610 restraints weight = 7564.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.182205 restraints weight = 6373.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.184614 restraints weight = 4163.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184185 restraints weight = 3183.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.184370 restraints weight = 3348.876| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7680 Z= 0.170 Angle : 0.717 8.998 10527 Z= 0.369 Chirality : 0.045 0.196 1265 Planarity : 0.006 0.074 1295 Dihedral : 9.838 58.151 1158 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.24 % Allowed : 16.74 % Favored : 77.02 % 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: 0.53 (0.26), residues: 984 helix: 1.35 (0.20), residues: 606 sheet: 0.29 (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 0.033 0.002 PHE A1133 TRP 0.023 0.002 TRP A 373 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 7674) covalent geometry : angle 0.71436 / 0.37 (10512) SS BOND : bond 0.00173 / 0.08 ( 3) SS BOND : angle 1.82913 / 0.67 ( 6) hydrogen bonds : bond 0.06179 / 4.17 ( 465) hydrogen bonds : angle 5.10564 / 3.59 ( 1362) link_BETA1-4 : bond 0.00105 / 0.06 ( 1) link_BETA1-4 : angle 0.90063 / 0.51 ( 3) link_NAG-ASN : bond 0.00228 / 0.12 ( 2) link_NAG-ASN : angle 1.90306 / 1.08 ( 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: 44 poor density : 133 time to evaluate : 0.328 Fit side-chains REVERT: A 178 MET cc_start: 0.7898 (ttm) cc_final: 0.7630 (ttm) REVERT: A 259 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.5617 (t80) REVERT: A 373 TRP cc_start: 0.6211 (t-100) cc_final: 0.5937 (t-100) REVERT: A 479 ILE cc_start: 0.9153 (mt) cc_final: 0.8880 (mt) REVERT: A 519 PHE cc_start: 0.7472 (t80) cc_final: 0.7100 (t80) REVERT: A 588 ARG cc_start: 0.7580 (tmm-80) cc_final: 0.6923 (mpt180) REVERT: A 797 ASP cc_start: 0.7457 (p0) cc_final: 0.6962 (p0) REVERT: A 949 ILE cc_start: 0.7207 (mm) cc_final: 0.6936 (mm) REVERT: A 1134 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 44 outliers final: 25 residues processed: 164 average time/residue: 0.0769 time to fit residues: 17.9500 Evaluate side-chains 142 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 425 VAL 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 744 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 1133 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 506 HIS A 901 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.221646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.176541 restraints weight = 7435.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179230 restraints weight = 6529.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181793 restraints weight = 4330.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181782 restraints weight = 3314.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181862 restraints weight = 3263.509| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7680 Z= 0.152 Angle : 0.640 8.050 10527 Z= 0.327 Chirality : 0.042 0.198 1265 Planarity : 0.006 0.054 1295 Dihedral : 8.238 58.543 1127 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.39 % Allowed : 17.87 % Favored : 76.74 % 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: 0.64 (0.26), residues: 984 helix: 1.42 (0.20), residues: 596 sheet: 0.25 (0.71), residues: 48 loop : -1.34 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.030 0.001 TYR A 190 PHE 0.030 0.002 PHE A1133 TRP 0.019 0.002 TRP A 64 HIS 0.007 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 7674) covalent geometry : angle 0.63773 / 0.33 (10512) SS BOND : bond 0.01188 / 0.57 ( 3) SS BOND : angle 1.20233 / 0.43 ( 6) hydrogen bonds : bond 0.05255 / 3.53 ( 465) hydrogen bonds : angle 4.83883 / 3.40 ( 1362) link_BETA1-4 : bond 0.00300 / 0.16 ( 1) link_BETA1-4 : angle 1.08604 / 0.59 ( 3) link_NAG-ASN : bond 0.00229 / 0.11 ( 2) link_NAG-ASN : angle 1.72275 / 0.98 ( 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 167 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.252 Fit side-chains REVERT: A 179 TYR cc_start: 0.7057 (m-80) cc_final: 0.6646 (m-80) REVERT: A 259 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5027 (t80) REVERT: A 479 ILE cc_start: 0.9173 (mt) cc_final: 0.8931 (mt) REVERT: A 588 ARG cc_start: 0.7601 (tmm-80) cc_final: 0.6894 (mmt-90) REVERT: A 797 ASP cc_start: 0.7216 (p0) cc_final: 0.6967 (p0) REVERT: A 901 ASN cc_start: 0.8418 (t0) cc_final: 0.8195 (t0) REVERT: A 1134 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7775 (mp) REVERT: A 1145 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8160 (tp) outliers start: 38 outliers final: 27 residues processed: 160 average time/residue: 0.0790 time to fit residues: 17.7231 Evaluate side-chains 143 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 310 ASN Chi-restraints excluded: chain A residue 314 GLN 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 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 1133 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1145 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: 2.9990 chunk 87 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 0.0970 chunk 89 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.225501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.182642 restraints weight = 7561.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.182861 restraints weight = 7565.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186357 restraints weight = 5850.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186238 restraints weight = 4005.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.186849 restraints weight = 3598.274| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7680 Z= 0.129 Angle : 0.604 8.373 10527 Z= 0.302 Chirality : 0.041 0.198 1265 Planarity : 0.005 0.051 1295 Dihedral : 7.884 59.251 1127 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.25 % Allowed : 20.00 % Favored : 74.75 % 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: 0.76 (0.26), residues: 984 helix: 1.59 (0.21), residues: 596 sheet: 0.27 (0.72), residues: 48 loop : -1.46 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 892 TYR 0.025 0.001 TYR A 190 PHE 0.023 0.001 PHE A1133 TRP 0.025 0.001 TRP A 64 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 7674) covalent geometry : angle 0.60228 / 0.30 (10512) SS BOND : bond 0.00551 / 0.26 ( 3) SS BOND : angle 1.18663 / 0.43 ( 6) hydrogen bonds : bond 0.04521 / 3.03 ( 465) hydrogen bonds : angle 4.60724 / 3.25 ( 1362) link_BETA1-4 : bond 0.00366 / 0.19 ( 1) link_BETA1-4 : angle 1.05840 / 0.56 ( 3) link_NAG-ASN : bond 0.00229 / 0.11 ( 2) link_NAG-ASN : angle 1.57388 / 0.89 ( 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 161 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 231 THR cc_start: 0.8630 (t) cc_final: 0.8364 (p) REVERT: A 259 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.4812 (t80) REVERT: A 450 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7838 (ptpp) REVERT: A 479 ILE cc_start: 0.9187 (mt) cc_final: 0.8922 (mt) REVERT: A 494 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5999 (tp) REVERT: A 588 ARG cc_start: 0.7474 (tmm-80) cc_final: 0.6774 (mpt180) REVERT: A 797 ASP cc_start: 0.7124 (p0) cc_final: 0.6826 (p0) REVERT: A 908 TYR cc_start: 0.8368 (m-80) cc_final: 0.8077 (m-80) outliers start: 37 outliers final: 23 residues processed: 153 average time/residue: 0.0722 time to fit residues: 15.8916 Evaluate side-chains 142 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 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 114 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 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 444 LEU Chi-restraints excluded: chain A residue 450 LYS 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 494 LEU Chi-restraints excluded: chain A residue 530 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 1133 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: 6.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.222478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.178992 restraints weight = 7534.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178744 restraints weight = 7844.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.182876 restraints weight = 5471.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182197 restraints weight = 4378.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.182575 restraints weight = 4000.389| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4270 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= 0.143 Angle : 0.620 9.473 10527 Z= 0.307 Chirality : 0.042 0.268 1265 Planarity : 0.005 0.056 1295 Dihedral : 7.367 56.090 1125 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.96 % Allowed : 21.70 % Favored : 73.33 % 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: 0.81 (0.26), residues: 984 helix: 1.63 (0.21), residues: 596 sheet: 0.27 (0.75), residues: 48 loop : -1.44 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1011 TYR 0.020 0.001 TYR A 190 PHE 0.024 0.001 PHE A1133 TRP 0.017 0.001 TRP A 64 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7674) covalent geometry : angle 0.61890 / 0.31 (10512) SS BOND : bond 0.00473 / 0.23 ( 3) SS BOND : angle 0.79516 / 0.37 ( 6) hydrogen bonds : bond 0.04628 / 3.10 ( 465) hydrogen bonds : angle 4.54357 / 3.22 ( 1362) link_BETA1-4 : bond 0.00458 / 0.24 ( 1) link_BETA1-4 : angle 1.19257 / 0.63 ( 3) link_NAG-ASN : bond 0.00219 / 0.11 ( 2) link_NAG-ASN : angle 1.53163 / 0.86 ( 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 156 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7680 (t80) cc_final: 0.7374 (t80) REVERT: A 259 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.4656 (t80) REVERT: A 403 GLN cc_start: 0.6872 (mm110) cc_final: 0.6644 (mm110) REVERT: A 479 ILE cc_start: 0.9190 (mt) cc_final: 0.8972 (mt) REVERT: A 588 ARG cc_start: 0.7553 (tmm-80) cc_final: 0.6946 (mpt180) REVERT: A 797 ASP cc_start: 0.7113 (p0) cc_final: 0.6866 (p0) outliers start: 35 outliers final: 22 residues processed: 147 average time/residue: 0.0742 time to fit residues: 15.5433 Evaluate side-chains 134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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 455 VAL 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 1108 MET 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 1133 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: 0.1980 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 GLN A 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.228841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.185777 restraints weight = 7601.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.184851 restraints weight = 8325.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.190653 restraints weight = 6086.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190081 restraints weight = 3323.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.190515 restraints weight = 3037.699| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4586 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= 0.126 Angle : 0.599 9.269 10527 Z= 0.295 Chirality : 0.041 0.198 1265 Planarity : 0.005 0.058 1295 Dihedral : 7.181 57.268 1125 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.69 % Allowed : 23.12 % Favored : 73.19 % 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: 0.86 (0.26), residues: 984 helix: 1.71 (0.21), residues: 599 sheet: 0.25 (0.78), residues: 48 loop : -1.53 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 892 TYR 0.018 0.001 TYR A 190 PHE 0.019 0.001 PHE A1133 TRP 0.014 0.001 TRP A 64 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 7674) covalent geometry : angle 0.59567 / 0.29 (10512) SS BOND : bond 0.00448 / 0.21 ( 3) SS BOND : angle 2.14979 / 0.81 ( 6) hydrogen bonds : bond 0.04325 / 2.90 ( 465) hydrogen bonds : angle 4.46017 / 3.16 ( 1362) link_BETA1-4 : bond 0.00358 / 0.19 ( 1) link_BETA1-4 : angle 1.16436 / 0.63 ( 3) link_NAG-ASN : bond 0.00219 / 0.11 ( 2) link_NAG-ASN : angle 1.41924 / 0.80 ( 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 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7520 (mm-40) REVERT: A 259 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.4833 (t80) REVERT: A 403 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6592 (mm110) REVERT: A 479 ILE cc_start: 0.9216 (mt) cc_final: 0.8977 (mt) REVERT: A 585 ASP cc_start: 0.7826 (t0) cc_final: 0.7499 (t0) REVERT: A 588 ARG cc_start: 0.7570 (tmm-80) cc_final: 0.6846 (mpt180) REVERT: A 949 ILE cc_start: 0.6539 (mm) cc_final: 0.6243 (mm) REVERT: A 1142 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7253 (mt) outliers start: 26 outliers final: 17 residues processed: 136 average time/residue: 0.0768 time to fit residues: 14.8363 Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 259 TYR 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 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 1108 MET 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: 0.0060 chunk 21 optimal weight: 0.0770 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.231412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.187961 restraints weight = 7524.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.187440 restraints weight = 7526.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.190774 restraints weight = 6158.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.190996 restraints weight = 4394.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.191555 restraints weight = 3782.173| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7680 Z= 0.119 Angle : 0.594 9.532 10527 Z= 0.292 Chirality : 0.040 0.190 1265 Planarity : 0.005 0.058 1295 Dihedral : 6.698 55.560 1123 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.55 % Allowed : 23.69 % Favored : 72.77 % 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: 0.98 (0.26), residues: 984 helix: 1.76 (0.20), residues: 605 sheet: 0.10 (0.76), residues: 48 loop : -1.41 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 892 TYR 0.031 0.001 TYR A 190 PHE 0.025 0.001 PHE A 786 TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 7674) covalent geometry : angle 0.59283 / 0.29 (10512) SS BOND : bond 0.00380 / 0.18 ( 3) SS BOND : angle 1.32158 / 0.69 ( 6) hydrogen bonds : bond 0.04081 / 2.74 ( 465) hydrogen bonds : angle 4.36384 / 3.10 ( 1362) link_BETA1-4 : bond 0.00324 / 0.17 ( 1) link_BETA1-4 : angle 1.13389 / 0.61 ( 3) link_NAG-ASN : bond 0.00246 / 0.12 ( 2) link_NAG-ASN : angle 1.31401 / 0.75 ( 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 136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 259 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.4585 (t80) REVERT: A 270 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8809 (mtpt) REVERT: A 479 ILE cc_start: 0.9233 (mt) cc_final: 0.8972 (mt) REVERT: A 585 ASP cc_start: 0.7764 (t0) cc_final: 0.7350 (t0) REVERT: A 588 ARG cc_start: 0.7565 (tmm-80) cc_final: 0.6855 (mpt180) REVERT: A 1142 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7270 (mt) outliers start: 25 outliers final: 19 residues processed: 131 average time/residue: 0.0747 time to fit residues: 14.1049 Evaluate side-chains 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 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 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 450 LYS 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 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1108 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 95 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.232174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.190389 restraints weight = 7691.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188742 restraints weight = 8909.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.193916 restraints weight = 6724.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.193167 restraints weight = 4082.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.193875 restraints weight = 3719.751| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7680 Z= 0.115 Angle : 0.573 8.834 10527 Z= 0.282 Chirality : 0.040 0.188 1265 Planarity : 0.005 0.059 1295 Dihedral : 6.504 56.652 1123 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.55 % Allowed : 24.26 % Favored : 72.20 % 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: 1.08 (0.27), residues: 984 helix: 1.85 (0.20), residues: 605 sheet: 0.04 (0.77), residues: 48 loop : -1.36 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 892 TYR 0.026 0.001 TYR A 190 PHE 0.016 0.001 PHE A1133 TRP 0.013 0.001 TRP A 373 HIS 0.004 0.000 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 7674) covalent geometry : angle 0.57235 / 0.28 (10512) SS BOND : bond 0.00388 / 0.18 ( 3) SS BOND : angle 0.83453 / 0.48 ( 6) hydrogen bonds : bond 0.03983 / 2.67 ( 465) hydrogen bonds : angle 4.31331 / 3.07 ( 1362) link_BETA1-4 : bond 0.00354 / 0.19 ( 1) link_BETA1-4 : angle 1.14649 / 0.62 ( 3) link_NAG-ASN : bond 0.00260 / 0.13 ( 2) link_NAG-ASN : angle 1.23494 / 0.71 ( 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 136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.4383 (t80) REVERT: A 479 ILE cc_start: 0.9246 (mt) cc_final: 0.8997 (mt) REVERT: A 547 MET cc_start: 0.7245 (tpp) cc_final: 0.6835 (mmt) REVERT: A 585 ASP cc_start: 0.7747 (t0) cc_final: 0.7341 (t0) REVERT: A 588 ARG cc_start: 0.7569 (tmm-80) cc_final: 0.6873 (mpt180) REVERT: A 1142 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7070 (mt) outliers start: 25 outliers final: 19 residues processed: 129 average time/residue: 0.0756 time to fit residues: 13.9758 Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 158 THR 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 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 450 LYS 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 775 ASP Chi-restraints excluded: chain A residue 1108 MET 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 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: 0.6980 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.231227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187840 restraints weight = 7517.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.186479 restraints weight = 8882.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.191455 restraints weight = 6673.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.190388 restraints weight = 4343.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.190830 restraints weight = 3649.886| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5177 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 : 0.585 9.225 10527 Z= 0.288 Chirality : 0.040 0.187 1265 Planarity : 0.005 0.060 1295 Dihedral : 6.274 58.301 1121 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.69 % Allowed : 24.40 % Favored : 71.91 % 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: 1.09 (0.27), residues: 984 helix: 1.82 (0.21), residues: 607 sheet: 0.05 (0.78), residues: 48 loop : -1.32 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 427 TYR 0.026 0.001 TYR A 190 PHE 0.025 0.001 PHE A 786 TRP 0.010 0.001 TRP A 373 HIS 0.003 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7674) covalent geometry : angle 0.58449 / 0.29 (10512) SS BOND : bond 0.00300 / 0.14 ( 3) SS BOND : angle 0.65899 / 0.34 ( 6) hydrogen bonds : bond 0.04083 / 2.74 ( 465) hydrogen bonds : angle 4.31843 / 3.07 ( 1362) link_BETA1-4 : bond 0.00321 / 0.17 ( 1) link_BETA1-4 : angle 1.10137 / 0.59 ( 3) link_NAG-ASN : bond 0.00219 / 0.11 ( 2) link_NAG-ASN : angle 1.19685 / 0.68 ( 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 140 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.5610 (OUTLIER) cc_final: 0.4220 (t80) REVERT: A 479 ILE cc_start: 0.9265 (mt) cc_final: 0.9025 (mt) REVERT: A 547 MET cc_start: 0.7298 (tpp) cc_final: 0.6877 (mmt) REVERT: A 585 ASP cc_start: 0.7720 (t0) cc_final: 0.7273 (t0) REVERT: A 588 ARG cc_start: 0.7557 (tmm-80) cc_final: 0.6834 (mpt180) REVERT: A 1142 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7258 (mt) outliers start: 26 outliers final: 21 residues processed: 133 average time/residue: 0.0762 time to fit residues: 14.5574 Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 186 GLU 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 425 VAL Chi-restraints excluded: chain A residue 450 LYS 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 763 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1108 MET 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 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: 5.9990 chunk 58 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 66 optimal weight: 7.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 170 GLN A 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.230734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.186896 restraints weight = 7546.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186052 restraints weight = 8445.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.192427 restraints weight = 5898.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.191863 restraints weight = 3319.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191845 restraints weight = 3277.604| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5314 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= 0.124 Angle : 0.602 10.131 10527 Z= 0.296 Chirality : 0.041 0.185 1265 Planarity : 0.005 0.059 1295 Dihedral : 6.306 59.040 1121 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.88 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: 1.12 (0.27), residues: 984 helix: 1.84 (0.21), residues: 608 sheet: 0.03 (0.79), residues: 48 loop : -1.30 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 892 TYR 0.025 0.001 TYR A 190 PHE 0.019 0.001 PHE A1133 TRP 0.016 0.001 TRP A 934 HIS 0.002 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7674) covalent geometry : angle 0.60179 / 0.30 (10512) SS BOND : bond 0.00317 / 0.15 ( 3) SS BOND : angle 0.60786 / 0.33 ( 6) hydrogen bonds : bond 0.04096 / 2.75 ( 465) hydrogen bonds : angle 4.32723 / 3.09 ( 1362) link_BETA1-4 : bond 0.00236 / 0.12 ( 1) link_BETA1-4 : angle 1.02085 / 0.54 ( 3) link_NAG-ASN : bond 0.00220 / 0.11 ( 2) link_NAG-ASN : angle 1.18854 / 0.67 ( 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 136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.4245 (t80) REVERT: A 444 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7577 (mp) REVERT: A 479 ILE cc_start: 0.9266 (mt) cc_final: 0.9029 (mt) REVERT: A 547 MET cc_start: 0.7226 (tpp) cc_final: 0.6855 (mmt) REVERT: A 585 ASP cc_start: 0.7709 (t0) cc_final: 0.7262 (t0) REVERT: A 588 ARG cc_start: 0.7561 (tmm-80) cc_final: 0.6824 (mpt180) REVERT: A 1142 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7252 (mt) outliers start: 27 outliers final: 21 residues processed: 129 average time/residue: 0.0766 time to fit residues: 13.9887 Evaluate side-chains 131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 157 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 186 GLU 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 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 455 VAL 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 867 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 81 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.233200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196148 restraints weight = 7470.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194668 restraints weight = 8768.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.197309 restraints weight = 7032.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.195543 restraints weight = 5122.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.196257 restraints weight = 4418.939| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7680 Z= 0.124 Angle : 0.608 11.596 10527 Z= 0.299 Chirality : 0.040 0.184 1265 Planarity : 0.005 0.060 1295 Dihedral : 6.247 59.191 1121 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.69 % Allowed : 25.25 % Favored : 71.06 % 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: 1.10 (0.27), residues: 984 helix: 1.83 (0.21), residues: 608 sheet: 0.05 (0.79), residues: 48 loop : -1.32 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 892 TYR 0.038 0.002 TYR A 908 PHE 0.026 0.001 PHE A 786 TRP 0.014 0.001 TRP A 934 HIS 0.002 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7674) covalent geometry : angle 0.60773 / 0.30 (10512) SS BOND : bond 0.00321 / 0.15 ( 3) SS BOND : angle 0.51323 / 0.27 ( 6) hydrogen bonds : bond 0.04066 / 2.73 ( 465) hydrogen bonds : angle 4.31119 / 3.07 ( 1362) link_BETA1-4 : bond 0.00347 / 0.18 ( 1) link_BETA1-4 : angle 1.11670 / 0.59 ( 3) link_NAG-ASN : bond 0.00215 / 0.11 ( 2) link_NAG-ASN : angle 1.17158 / 0.66 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.09 seconds wall clock time: 25 minutes 47.25 seconds (1547.25 seconds total)