Starting phenix.real_space_refine on Fri Jul 25 15:03:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9q_36995/07_2025/8k9q_36995_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9q_36995/07_2025/8k9q_36995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k9q_36995/07_2025/8k9q_36995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9q_36995/07_2025/8k9q_36995.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9q_36995/07_2025/8k9q_36995_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9q_36995/07_2025/8k9q_36995_neut.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.173 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 2 5.49 5 S 35 5.16 5 C 4932 2.51 5 N 1240 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7549 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7340 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 55, 'TRANS': 871} Chain breaks: 5 Chain: "A" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {'D39': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.10, per 1000 atoms: 0.68 Number of scatterers: 7549 At special positions: 0 Unit cell: (79.04, 92.352, 128.128, 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 35 16.00 P 2 15.00 O 1340 8.00 N 1240 7.00 C 4932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 449 " distance=2.01 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 606 " distance=2.01 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 793 " distance=2.05 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 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 849.8 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 46.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 146 through 169 Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.690A pdb=" N GLN A 236 " --> pdb=" O SER A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.716A pdb=" N PHE A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.685A pdb=" N LEU A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.622A pdb=" N PHE A 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 281 through 301 removed outlier: 3.821A pdb=" N LEU A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 removed outlier: 4.235A pdb=" N LEU A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.518A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 385 " --> pdb=" O HIS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.272A pdb=" N LEU A 406 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.742A pdb=" N SER A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.503A pdb=" N TRP A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 461 removed outlier: 3.668A pdb=" N VAL A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 610 through 613 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 645 through 649 Processing helix chain 'A' and resid 675 through 678 No H-bonds generated for 'chain 'A' and resid 675 through 678' Processing helix chain 'A' and resid 685 through 693 Processing helix chain 'A' and resid 804 through 810 removed outlier: 3.764A pdb=" N GLY A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 816 removed outlier: 4.172A pdb=" N MET A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 843 removed outlier: 3.714A pdb=" N PHE A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 828 " --> pdb=" O PRO A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 858 removed outlier: 3.682A pdb=" N GLN A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 898 through 902 removed outlier: 3.520A pdb=" N ASP A 901 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 902 " --> pdb=" O GLN A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 898 through 902' Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 913 through 954 removed outlier: 3.516A pdb=" N CYS A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 930 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 992 Processing helix chain 'A' and resid 995 through 1022 removed outlier: 3.614A pdb=" N ALA A 999 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1042 removed outlier: 3.560A pdb=" N TRP A1042 " --> pdb=" O ILE A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1048 Processing helix chain 'A' and resid 1048 through 1059 removed outlier: 3.608A pdb=" N VAL A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1074 Processing helix chain 'A' and resid 1075 through 1084 Processing helix chain 'A' and resid 1103 through 1124 Processing helix chain 'A' and resid 1128 through 1131 Processing helix chain 'A' and resid 1132 through 1150 removed outlier: 3.800A pdb=" N LEU A1138 " --> pdb=" O GLN A1134 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A1150 " --> pdb=" O VAL A1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 4.911A pdb=" N PHE A 268 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 222 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE A 269 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 224 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL A 271 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE A 226 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 324 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 225 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N HIS A 326 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 227 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 321 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ILE A 351 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 323 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N MET A 353 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 325 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 348 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 399 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 350 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 401 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR A 352 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 505 through 506 Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 528 removed outlier: 3.655A pdb=" N GLU A 527 " --> pdb=" O GLY A 666 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY A 666 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 681 Processing sheet with id=AA5, first strand: chain 'A' and resid 694 through 698 removed outlier: 3.501A pdb=" N ILE A 797 " --> pdb=" O LEU A 698 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 972 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: 2.29 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1153 1.27 - 1.41: 1954 1.41 - 1.54: 4545 1.54 - 1.68: 35 1.68 - 1.81: 59 Bond restraints: 7746 Sorted by residual: bond pdb=" C TYR A 813 " pdb=" O TYR A 813 " ideal model delta sigma weight residual 1.237 1.137 0.099 1.17e-02 7.31e+03 7.22e+01 bond pdb=" C GLN A 742 " pdb=" O GLN A 742 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.22e-02 6.72e+03 5.84e+01 bond pdb=" C TYR A 748 " pdb=" O TYR A 748 " ideal model delta sigma weight residual 1.233 1.137 0.096 1.29e-02 6.01e+03 5.53e+01 bond pdb=" C GLY A 765 " pdb=" O GLY A 765 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.09e-02 8.42e+03 5.50e+01 bond pdb=" C LEU A 812 " pdb=" O LEU A 812 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.26e-02 6.30e+03 5.26e+01 ... (remaining 7741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 9848 3.62 - 7.24: 669 7.24 - 10.86: 35 10.86 - 14.48: 2 14.48 - 18.10: 2 Bond angle restraints: 10556 Sorted by residual: angle pdb=" C GLY A1125 " pdb=" N VAL A1126 " pdb=" CA VAL A1126 " ideal model delta sigma weight residual 122.35 111.78 10.57 1.18e+00 7.18e-01 8.02e+01 angle pdb=" N ILE A 508 " pdb=" CA ILE A 508 " pdb=" C ILE A 508 " ideal model delta sigma weight residual 113.47 105.92 7.55 1.01e+00 9.80e-01 5.59e+01 angle pdb=" N LEU A 252 " pdb=" CA LEU A 252 " pdb=" C LEU A 252 " ideal model delta sigma weight residual 111.36 119.22 -7.86 1.09e+00 8.42e-01 5.20e+01 angle pdb=" CA TYR A 813 " pdb=" C TYR A 813 " pdb=" O TYR A 813 " ideal model delta sigma weight residual 120.55 113.03 7.52 1.06e+00 8.90e-01 5.04e+01 angle pdb=" N MET A 993 " pdb=" CA MET A 993 " pdb=" C MET A 993 " ideal model delta sigma weight residual 111.52 121.37 -9.85 1.40e+00 5.10e-01 4.95e+01 ... (remaining 10551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.91: 4459 29.91 - 59.82: 298 59.82 - 89.73: 29 89.73 - 119.64: 4 119.64 - 149.55: 3 Dihedral angle restraints: 4793 sinusoidal: 2069 harmonic: 2724 Sorted by residual: dihedral pdb=" CB CYS A 177 " pdb=" SG CYS A 177 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual -86.00 -170.58 84.58 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" C GLU A 746 " pdb=" N GLU A 746 " pdb=" CA GLU A 746 " pdb=" CB GLU A 746 " ideal model delta harmonic sigma weight residual -122.60 -142.14 19.54 0 2.50e+00 1.60e-01 6.11e+01 dihedral pdb=" N GLU A 746 " pdb=" C GLU A 746 " pdb=" CA GLU A 746 " pdb=" CB GLU A 746 " ideal model delta harmonic sigma weight residual 122.80 141.43 -18.63 0 2.50e+00 1.60e-01 5.55e+01 ... (remaining 4790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 993 0.157 - 0.313: 215 0.313 - 0.469: 18 0.469 - 0.626: 1 0.626 - 0.782: 1 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA GLU A 746 " pdb=" N GLU A 746 " pdb=" C GLU A 746 " pdb=" CB GLU A 746 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PRO A 768 " pdb=" N PRO A 768 " pdb=" C PRO A 768 " pdb=" CB PRO A 768 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.61 2.00e-01 2.50e+01 9.44e+00 chirality pdb=" CA SER A 346 " pdb=" N SER A 346 " pdb=" C SER A 346 " pdb=" CB SER A 346 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 1225 not shown) Planarity restraints: 1304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 D39 A1504 " 0.100 2.00e-02 2.50e+03 2.41e-01 5.78e+02 pdb=" C29 D39 A1504 " -0.324 2.00e-02 2.50e+03 pdb=" C30 D39 A1504 " 0.326 2.00e-02 2.50e+03 pdb=" C31 D39 A1504 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 468 " 0.022 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ARG A 468 " -0.081 2.00e-02 2.50e+03 pdb=" O ARG A 468 " 0.031 2.00e-02 2.50e+03 pdb=" N ALA A 469 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 642 " 0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C GLU A 642 " -0.071 2.00e-02 2.50e+03 pdb=" O GLU A 642 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 643 " 0.024 2.00e-02 2.50e+03 ... (remaining 1301 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2156 2.82 - 3.34: 6855 3.34 - 3.86: 12788 3.86 - 4.38: 15773 4.38 - 4.90: 25685 Nonbonded interactions: 63257 Sorted by model distance: nonbonded pdb=" O ASP A 216 " pdb=" OD1 ASP A 216 " model vdw 2.303 3.040 nonbonded pdb=" O VAL A1146 " pdb=" OG1 THR A1149 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 716 " pdb=" NH2 ARG A 815 " model vdw 2.337 3.120 nonbonded pdb=" NE2 GLN A 835 " pdb=" O ILE A 846 " model vdw 2.374 3.120 nonbonded pdb=" O4 D39 A1504 " pdb=" O6 D39 A1504 " model vdw 2.404 2.432 ... (remaining 63252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.015 0.099 7749 Z= 1.096 Angle : 1.923 18.099 10562 Z= 1.377 Chirality : 0.124 0.782 1228 Planarity : 0.011 0.241 1304 Dihedral : 18.916 149.553 3014 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 6.84 % Allowed : 14.77 % Favored : 78.39 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.26), residues: 915 helix: -0.49 (0.26), residues: 350 sheet: -0.52 (0.37), residues: 167 loop : -0.83 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 448 HIS 0.015 0.002 HIS A 764 PHE 0.030 0.004 PHE A 427 TYR 0.055 0.004 TYR A 748 ARG 0.005 0.001 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.22050 ( 341) hydrogen bonds : angle 8.25849 ( 972) SS BOND : bond 0.01893 ( 3) SS BOND : angle 4.50526 ( 6) covalent geometry : bond 0.01492 ( 7746) covalent geometry : angle 1.92091 (10556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.798 Fit side-chains REVERT: A 154 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7559 (tp) REVERT: A 175 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8217 (mtmt) REVERT: A 207 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 311 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7575 (ptt90) REVERT: A 501 SER cc_start: 0.6900 (t) cc_final: 0.6562 (p) REVERT: A 506 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.4234 (tp) REVERT: A 559 LYS cc_start: 0.7301 (tttm) cc_final: 0.6975 (tptp) REVERT: A 645 LEU cc_start: 0.7460 (tp) cc_final: 0.6998 (tp) REVERT: A 652 GLN cc_start: 0.6972 (mt0) cc_final: 0.6114 (mm-40) REVERT: A 657 ILE cc_start: 0.7947 (mt) cc_final: 0.7648 (mm) REVERT: A 687 ARG cc_start: 0.7323 (mmt180) cc_final: 0.7118 (tpt90) REVERT: A 790 ASP cc_start: 0.8137 (t70) cc_final: 0.7904 (t0) REVERT: A 863 MET cc_start: 0.8349 (tpp) cc_final: 0.7767 (mmt) REVERT: A 927 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8066 (m) REVERT: A 1076 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6816 (tpp) outliers start: 56 outliers final: 10 residues processed: 218 average time/residue: 1.0046 time to fit residues: 234.1259 Evaluate side-chains 135 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 311 ARG Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 230 ASN A 274 ASN A 348 ASN A 391 ASN A 675 HIS A 677 ASN A 786 GLN A 898 HIS A 899 GLN A 900 ASN A1047 ASN A1069 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117201 restraints weight = 8465.412| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.76 r_work: 0.3156 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7749 Z= 0.171 Angle : 0.678 7.667 10562 Z= 0.342 Chirality : 0.045 0.210 1228 Planarity : 0.005 0.047 1304 Dihedral : 13.947 101.706 1346 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 5.86 % Allowed : 19.54 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 915 helix: 1.02 (0.26), residues: 371 sheet: -0.31 (0.38), residues: 164 loop : -0.22 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 448 HIS 0.004 0.001 HIS A 683 PHE 0.021 0.002 PHE A 826 TYR 0.014 0.002 TYR A 643 ARG 0.005 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 341) hydrogen bonds : angle 5.08699 ( 972) SS BOND : bond 0.00946 ( 3) SS BOND : angle 3.15600 ( 6) covalent geometry : bond 0.00406 ( 7746) covalent geometry : angle 0.67419 (10556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.792 Fit side-chains REVERT: A 175 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8499 (mtmt) REVERT: A 216 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6457 (t70) REVERT: A 310 GLU cc_start: 0.7495 (tt0) cc_final: 0.6909 (tm-30) REVERT: A 317 ASP cc_start: 0.7821 (m-30) cc_final: 0.7423 (p0) REVERT: A 471 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: A 559 LYS cc_start: 0.7589 (tttm) cc_final: 0.7103 (tptp) REVERT: A 645 LEU cc_start: 0.7291 (tp) cc_final: 0.6825 (tp) REVERT: A 652 GLN cc_start: 0.6886 (mt0) cc_final: 0.6185 (mm-40) REVERT: A 657 ILE cc_start: 0.7866 (mt) cc_final: 0.7578 (mm) REVERT: A 687 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7105 (tpt90) REVERT: A 757 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7663 (mmm160) REVERT: A 790 ASP cc_start: 0.8623 (t70) cc_final: 0.8161 (t0) REVERT: A 794 ASN cc_start: 0.6880 (t0) cc_final: 0.6524 (t0) REVERT: A 870 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7468 (mm) REVERT: A 1076 MET cc_start: 0.7923 (tpp) cc_final: 0.7534 (tpt) outliers start: 48 outliers final: 13 residues processed: 159 average time/residue: 1.0006 time to fit residues: 170.2580 Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1056 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 249 HIS A 677 ASN A 898 HIS A 900 ASN A1026 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.147487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116567 restraints weight = 8570.574| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.77 r_work: 0.3128 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7749 Z= 0.140 Angle : 0.599 7.632 10562 Z= 0.301 Chirality : 0.043 0.230 1228 Planarity : 0.005 0.047 1304 Dihedral : 12.338 82.604 1319 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.37 % Allowed : 19.78 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 915 helix: 1.51 (0.26), residues: 376 sheet: -0.08 (0.39), residues: 165 loop : 0.08 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 448 HIS 0.005 0.001 HIS A 675 PHE 0.021 0.001 PHE A 826 TYR 0.010 0.001 TYR A 643 ARG 0.003 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 341) hydrogen bonds : angle 4.64239 ( 972) SS BOND : bond 0.00615 ( 3) SS BOND : angle 3.39872 ( 6) covalent geometry : bond 0.00324 ( 7746) covalent geometry : angle 0.59392 (10556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.828 Fit side-chains REVERT: A 155 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7961 (tp) REVERT: A 175 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8397 (mtmt) REVERT: A 216 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6350 (t70) REVERT: A 310 GLU cc_start: 0.7430 (tt0) cc_final: 0.6806 (tm-30) REVERT: A 317 ASP cc_start: 0.7932 (m-30) cc_final: 0.7322 (p0) REVERT: A 471 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: A 501 SER cc_start: 0.6585 (t) cc_final: 0.6271 (p) REVERT: A 559 LYS cc_start: 0.7532 (tttm) cc_final: 0.6993 (tppt) REVERT: A 645 LEU cc_start: 0.7202 (tp) cc_final: 0.6703 (tp) REVERT: A 652 GLN cc_start: 0.6934 (mt0) cc_final: 0.6222 (mm110) REVERT: A 657 ILE cc_start: 0.7833 (mt) cc_final: 0.7568 (mm) REVERT: A 687 ARG cc_start: 0.7359 (mmt180) cc_final: 0.6934 (tpt90) REVERT: A 757 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7605 (mmm160) REVERT: A 790 ASP cc_start: 0.8590 (t70) cc_final: 0.8064 (t0) REVERT: A 794 ASN cc_start: 0.6801 (t0) cc_final: 0.5989 (t0) REVERT: A 863 MET cc_start: 0.8840 (mpp) cc_final: 0.8483 (mmt) REVERT: A 870 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7417 (mm) REVERT: A 1076 MET cc_start: 0.7879 (tpp) cc_final: 0.7492 (tpt) outliers start: 44 outliers final: 18 residues processed: 148 average time/residue: 1.0663 time to fit residues: 168.4173 Evaluate side-chains 126 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 677 ASN A 898 HIS ** A1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116365 restraints weight = 8593.666| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.76 r_work: 0.3152 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7749 Z= 0.134 Angle : 0.572 8.882 10562 Z= 0.287 Chirality : 0.043 0.239 1228 Planarity : 0.005 0.053 1304 Dihedral : 11.651 70.744 1316 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.88 % Allowed : 21.37 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.28), residues: 915 helix: 1.74 (0.26), residues: 376 sheet: 0.05 (0.40), residues: 165 loop : 0.00 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 PHE 0.020 0.001 PHE A 826 TYR 0.009 0.001 TYR A 996 ARG 0.005 0.000 ARG A 723 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 341) hydrogen bonds : angle 4.52837 ( 972) SS BOND : bond 0.00661 ( 3) SS BOND : angle 3.74364 ( 6) covalent geometry : bond 0.00315 ( 7746) covalent geometry : angle 0.56547 (10556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.793 Fit side-chains REVERT: A 155 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 175 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8401 (mtmt) REVERT: A 178 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7845 (mtm-85) REVERT: A 216 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6340 (t70) REVERT: A 310 GLU cc_start: 0.7439 (tt0) cc_final: 0.6790 (tm-30) REVERT: A 317 ASP cc_start: 0.7907 (m-30) cc_final: 0.7337 (p0) REVERT: A 462 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: A 471 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7418 (mt0) REVERT: A 501 SER cc_start: 0.6695 (t) cc_final: 0.6397 (p) REVERT: A 559 LYS cc_start: 0.7478 (tttm) cc_final: 0.6994 (tptp) REVERT: A 632 GLU cc_start: 0.7710 (pm20) cc_final: 0.7346 (pm20) REVERT: A 645 LEU cc_start: 0.7174 (tp) cc_final: 0.6710 (tp) REVERT: A 652 GLN cc_start: 0.6837 (mt0) cc_final: 0.6153 (mm110) REVERT: A 657 ILE cc_start: 0.7786 (mt) cc_final: 0.7583 (mm) REVERT: A 687 ARG cc_start: 0.7474 (mmt180) cc_final: 0.7061 (tpt90) REVERT: A 757 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7612 (mmm160) REVERT: A 790 ASP cc_start: 0.8533 (t70) cc_final: 0.8215 (t0) REVERT: A 794 ASN cc_start: 0.6435 (t0) cc_final: 0.5999 (t0) REVERT: A 863 MET cc_start: 0.8847 (mpp) cc_final: 0.8505 (mmt) REVERT: A 870 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7420 (mm) REVERT: A 993 MET cc_start: 0.5409 (ttt) cc_final: 0.4770 (ttp) REVERT: A 1076 MET cc_start: 0.7916 (tpp) cc_final: 0.7531 (tpt) outliers start: 40 outliers final: 20 residues processed: 141 average time/residue: 1.0462 time to fit residues: 157.2945 Evaluate side-chains 133 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1109 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 348 ASN A 385 GLN A 677 ASN A 898 HIS A1057 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.148715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118676 restraints weight = 8542.586| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.66 r_work: 0.3180 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7749 Z= 0.117 Angle : 0.552 7.677 10562 Z= 0.276 Chirality : 0.042 0.226 1228 Planarity : 0.004 0.048 1304 Dihedral : 10.548 58.625 1316 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.15 % Allowed : 22.10 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.28), residues: 915 helix: 1.88 (0.26), residues: 376 sheet: 0.19 (0.40), residues: 163 loop : 0.12 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 PHE 0.017 0.001 PHE A 826 TYR 0.008 0.001 TYR A 996 ARG 0.006 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 341) hydrogen bonds : angle 4.38161 ( 972) SS BOND : bond 0.00700 ( 3) SS BOND : angle 3.43143 ( 6) covalent geometry : bond 0.00273 ( 7746) covalent geometry : angle 0.54625 (10556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.872 Fit side-chains REVERT: A 155 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7976 (tp) REVERT: A 175 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8346 (mtmt) REVERT: A 216 ASP cc_start: 0.6916 (m-30) cc_final: 0.6377 (t70) REVERT: A 310 GLU cc_start: 0.7412 (tt0) cc_final: 0.6896 (tm-30) REVERT: A 317 ASP cc_start: 0.7858 (m-30) cc_final: 0.7369 (p0) REVERT: A 471 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7253 (mt0) REVERT: A 501 SER cc_start: 0.6719 (t) cc_final: 0.6483 (p) REVERT: A 559 LYS cc_start: 0.7563 (tttm) cc_final: 0.7052 (tptp) REVERT: A 632 GLU cc_start: 0.7757 (pm20) cc_final: 0.7506 (pm20) REVERT: A 645 LEU cc_start: 0.7193 (tp) cc_final: 0.6719 (tp) REVERT: A 652 GLN cc_start: 0.6818 (mt0) cc_final: 0.6155 (mm110) REVERT: A 656 VAL cc_start: 0.8229 (p) cc_final: 0.8001 (t) REVERT: A 687 ARG cc_start: 0.7482 (mmt180) cc_final: 0.7049 (tpt90) REVERT: A 757 ARG cc_start: 0.7806 (tpp80) cc_final: 0.7541 (mmm160) REVERT: A 790 ASP cc_start: 0.8536 (t70) cc_final: 0.8257 (t0) REVERT: A 870 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7553 (mm) REVERT: A 912 LEU cc_start: 0.7885 (mt) cc_final: 0.7678 (mm) REVERT: A 993 MET cc_start: 0.5457 (ttt) cc_final: 0.5219 (ttm) REVERT: A 1076 MET cc_start: 0.7857 (tpp) cc_final: 0.7452 (tpt) outliers start: 34 outliers final: 11 residues processed: 135 average time/residue: 1.1939 time to fit residues: 172.4332 Evaluate side-chains 117 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 63 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 677 ASN A 898 HIS A1057 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116707 restraints weight = 8418.874| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.78 r_work: 0.3155 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7749 Z= 0.131 Angle : 0.549 9.570 10562 Z= 0.278 Chirality : 0.042 0.232 1228 Planarity : 0.005 0.047 1304 Dihedral : 10.168 57.995 1315 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.64 % Allowed : 21.25 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 915 helix: 1.84 (0.26), residues: 379 sheet: 0.29 (0.40), residues: 163 loop : 0.15 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 PHE 0.020 0.001 PHE A 826 TYR 0.010 0.001 TYR A 996 ARG 0.006 0.000 ARG A1016 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 341) hydrogen bonds : angle 4.31765 ( 972) SS BOND : bond 0.00541 ( 3) SS BOND : angle 4.21222 ( 6) covalent geometry : bond 0.00312 ( 7746) covalent geometry : angle 0.54010 (10556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 1.285 Fit side-chains REVERT: A 155 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7939 (tp) REVERT: A 175 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8348 (mtmt) REVERT: A 216 ASP cc_start: 0.6922 (m-30) cc_final: 0.6352 (t70) REVERT: A 310 GLU cc_start: 0.7350 (tt0) cc_final: 0.6716 (tm-30) REVERT: A 317 ASP cc_start: 0.7898 (m-30) cc_final: 0.7196 (p0) REVERT: A 471 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: A 490 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8904 (mtm) REVERT: A 501 SER cc_start: 0.6638 (t) cc_final: 0.6353 (p) REVERT: A 559 LYS cc_start: 0.7507 (tttm) cc_final: 0.6994 (tptp) REVERT: A 632 GLU cc_start: 0.7818 (pm20) cc_final: 0.7576 (pm20) REVERT: A 645 LEU cc_start: 0.7158 (tp) cc_final: 0.6670 (tp) REVERT: A 652 GLN cc_start: 0.6936 (mt0) cc_final: 0.6217 (mm110) REVERT: A 687 ARG cc_start: 0.7447 (mmt180) cc_final: 0.6962 (tpt90) REVERT: A 757 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7542 (mmm160) REVERT: A 790 ASP cc_start: 0.8532 (t70) cc_final: 0.8223 (t0) REVERT: A 809 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7988 (tp) REVERT: A 863 MET cc_start: 0.8809 (mpp) cc_final: 0.8522 (mmt) REVERT: A 870 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7526 (mm) REVERT: A 903 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 912 LEU cc_start: 0.7886 (mt) cc_final: 0.7637 (mm) REVERT: A 993 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.5177 (ttm) REVERT: A 1076 MET cc_start: 0.7890 (tpp) cc_final: 0.7459 (tpt) outliers start: 38 outliers final: 15 residues processed: 133 average time/residue: 1.5086 time to fit residues: 213.7988 Evaluate side-chains 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 677 ASN A 898 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118148 restraints weight = 8343.727| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.77 r_work: 0.3179 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7749 Z= 0.112 Angle : 0.529 10.413 10562 Z= 0.267 Chirality : 0.041 0.251 1228 Planarity : 0.004 0.046 1304 Dihedral : 9.816 59.779 1315 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.66 % Allowed : 22.10 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.28), residues: 915 helix: 1.92 (0.27), residues: 379 sheet: 0.35 (0.41), residues: 163 loop : 0.22 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 448 HIS 0.004 0.000 HIS A 675 PHE 0.016 0.001 PHE A 826 TYR 0.007 0.001 TYR A 996 ARG 0.005 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 341) hydrogen bonds : angle 4.21432 ( 972) SS BOND : bond 0.00659 ( 3) SS BOND : angle 3.91771 ( 6) covalent geometry : bond 0.00265 ( 7746) covalent geometry : angle 0.52076 (10556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.798 Fit side-chains REVERT: A 155 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7937 (tp) REVERT: A 175 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8332 (mtmt) REVERT: A 216 ASP cc_start: 0.6927 (m-30) cc_final: 0.6333 (t70) REVERT: A 310 GLU cc_start: 0.7336 (tt0) cc_final: 0.6790 (tm-30) REVERT: A 317 ASP cc_start: 0.7880 (m-30) cc_final: 0.7195 (p0) REVERT: A 320 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 471 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: A 490 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8894 (mtm) REVERT: A 501 SER cc_start: 0.6632 (t) cc_final: 0.6343 (p) REVERT: A 559 LYS cc_start: 0.7430 (tttm) cc_final: 0.6928 (tptp) REVERT: A 645 LEU cc_start: 0.7100 (tp) cc_final: 0.6625 (tp) REVERT: A 652 GLN cc_start: 0.6969 (mt0) cc_final: 0.6253 (mm110) REVERT: A 687 ARG cc_start: 0.7444 (mmt180) cc_final: 0.6950 (tpt90) REVERT: A 757 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7480 (mmm160) REVERT: A 790 ASP cc_start: 0.8548 (t70) cc_final: 0.8212 (t0) REVERT: A 863 MET cc_start: 0.8789 (mpp) cc_final: 0.8533 (mmt) REVERT: A 870 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7510 (mm) REVERT: A 912 LEU cc_start: 0.7742 (mt) cc_final: 0.7512 (mm) REVERT: A 1076 MET cc_start: 0.7868 (tpp) cc_final: 0.7447 (tpt) outliers start: 30 outliers final: 13 residues processed: 126 average time/residue: 1.1565 time to fit residues: 155.4471 Evaluate side-chains 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 898 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117207 restraints weight = 8553.537| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.77 r_work: 0.3152 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7749 Z= 0.131 Angle : 0.553 12.223 10562 Z= 0.280 Chirality : 0.042 0.251 1228 Planarity : 0.004 0.046 1304 Dihedral : 9.664 58.738 1315 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.42 % Allowed : 21.86 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 915 helix: 1.87 (0.27), residues: 379 sheet: 0.34 (0.40), residues: 165 loop : 0.18 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 PHE 0.021 0.001 PHE A 826 TYR 0.010 0.001 TYR A 996 ARG 0.006 0.000 ARG A1016 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 341) hydrogen bonds : angle 4.25004 ( 972) SS BOND : bond 0.00685 ( 3) SS BOND : angle 4.09171 ( 6) covalent geometry : bond 0.00316 ( 7746) covalent geometry : angle 0.54492 (10556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 2.079 Fit side-chains REVERT: A 155 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7962 (tp) REVERT: A 175 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8357 (mtmt) REVERT: A 216 ASP cc_start: 0.6874 (m-30) cc_final: 0.6291 (t70) REVERT: A 310 GLU cc_start: 0.7358 (tt0) cc_final: 0.6758 (tm-30) REVERT: A 317 ASP cc_start: 0.7912 (m-30) cc_final: 0.7205 (p0) REVERT: A 320 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8717 (m) REVERT: A 471 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: A 490 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8909 (mtm) REVERT: A 501 SER cc_start: 0.6705 (t) cc_final: 0.6407 (p) REVERT: A 559 LYS cc_start: 0.7408 (tttm) cc_final: 0.6926 (tptp) REVERT: A 645 LEU cc_start: 0.7153 (tp) cc_final: 0.6707 (tp) REVERT: A 652 GLN cc_start: 0.7035 (mt0) cc_final: 0.6259 (mm110) REVERT: A 687 ARG cc_start: 0.7445 (mmt180) cc_final: 0.6960 (tpt90) REVERT: A 757 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7528 (mmm160) REVERT: A 790 ASP cc_start: 0.8521 (t70) cc_final: 0.8224 (t0) REVERT: A 863 MET cc_start: 0.8808 (mpp) cc_final: 0.8525 (mmt) REVERT: A 870 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7516 (mm) REVERT: A 912 LEU cc_start: 0.7804 (mt) cc_final: 0.7565 (mm) REVERT: A 1076 MET cc_start: 0.7900 (tpp) cc_final: 0.7473 (tpt) outliers start: 28 outliers final: 14 residues processed: 125 average time/residue: 1.5777 time to fit residues: 212.0695 Evaluate side-chains 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 898 HIS A1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118322 restraints weight = 8605.511| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.79 r_work: 0.3156 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7749 Z= 0.113 Angle : 0.542 13.004 10562 Z= 0.275 Chirality : 0.042 0.240 1228 Planarity : 0.004 0.046 1304 Dihedral : 9.354 58.982 1315 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.69 % Allowed : 23.08 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.28), residues: 915 helix: 2.00 (0.27), residues: 373 sheet: 0.38 (0.40), residues: 173 loop : 0.25 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 448 HIS 0.009 0.001 HIS A1108 PHE 0.017 0.001 PHE A 826 TYR 0.008 0.001 TYR A 996 ARG 0.007 0.000 ARG A1016 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 341) hydrogen bonds : angle 4.19127 ( 972) SS BOND : bond 0.00777 ( 3) SS BOND : angle 4.12413 ( 6) covalent geometry : bond 0.00271 ( 7746) covalent geometry : angle 0.53313 (10556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.211 Fit side-chains REVERT: A 155 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7977 (tp) REVERT: A 175 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8302 (mtmt) REVERT: A 310 GLU cc_start: 0.7303 (tt0) cc_final: 0.6945 (tt0) REVERT: A 317 ASP cc_start: 0.7907 (m-30) cc_final: 0.7202 (p0) REVERT: A 320 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8716 (m) REVERT: A 471 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: A 490 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8927 (mtm) REVERT: A 501 SER cc_start: 0.6689 (t) cc_final: 0.6391 (p) REVERT: A 559 LYS cc_start: 0.7398 (tttm) cc_final: 0.6870 (tptp) REVERT: A 645 LEU cc_start: 0.7121 (tp) cc_final: 0.6666 (tp) REVERT: A 652 GLN cc_start: 0.7043 (mt0) cc_final: 0.6257 (mm110) REVERT: A 687 ARG cc_start: 0.7395 (mmt180) cc_final: 0.6948 (tpt90) REVERT: A 757 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7482 (mmm160) REVERT: A 790 ASP cc_start: 0.8519 (t70) cc_final: 0.8192 (t0) REVERT: A 863 MET cc_start: 0.8787 (mpp) cc_final: 0.8527 (mmt) REVERT: A 870 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7472 (mm) REVERT: A 912 LEU cc_start: 0.7700 (mt) cc_final: 0.7472 (mm) REVERT: A 1076 MET cc_start: 0.7856 (tpp) cc_final: 0.7436 (tpt) outliers start: 22 outliers final: 13 residues processed: 116 average time/residue: 1.3523 time to fit residues: 166.7437 Evaluate side-chains 116 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 254 HIS A1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119106 restraints weight = 8485.853| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.78 r_work: 0.3169 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7749 Z= 0.109 Angle : 0.538 12.751 10562 Z= 0.274 Chirality : 0.042 0.228 1228 Planarity : 0.004 0.046 1304 Dihedral : 9.069 59.295 1315 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.08 % Allowed : 23.44 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 915 helix: 1.95 (0.27), residues: 379 sheet: 0.40 (0.40), residues: 173 loop : 0.29 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 448 HIS 0.013 0.001 HIS A1108 PHE 0.018 0.001 PHE A1141 TYR 0.007 0.001 TYR A 996 ARG 0.007 0.001 ARG A1016 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 341) hydrogen bonds : angle 4.11481 ( 972) SS BOND : bond 0.00770 ( 3) SS BOND : angle 3.77261 ( 6) covalent geometry : bond 0.00257 ( 7746) covalent geometry : angle 0.53057 (10556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.819 Fit side-chains REVERT: A 155 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7985 (tp) REVERT: A 175 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8289 (mtmt) REVERT: A 310 GLU cc_start: 0.7346 (tt0) cc_final: 0.6995 (tt0) REVERT: A 317 ASP cc_start: 0.7918 (m-30) cc_final: 0.7249 (p0) REVERT: A 320 SER cc_start: 0.9063 (p) cc_final: 0.8713 (m) REVERT: A 471 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: A 490 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8935 (mtm) REVERT: A 501 SER cc_start: 0.6690 (t) cc_final: 0.6406 (p) REVERT: A 559 LYS cc_start: 0.7403 (tttm) cc_final: 0.6902 (tptp) REVERT: A 645 LEU cc_start: 0.7128 (tp) cc_final: 0.6666 (tp) REVERT: A 652 GLN cc_start: 0.7066 (mt0) cc_final: 0.6268 (mm110) REVERT: A 687 ARG cc_start: 0.7370 (mmt180) cc_final: 0.6917 (tpt90) REVERT: A 757 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7432 (mmm160) REVERT: A 790 ASP cc_start: 0.8474 (t70) cc_final: 0.8166 (t0) REVERT: A 863 MET cc_start: 0.8760 (mpp) cc_final: 0.8533 (mmt) REVERT: A 870 LEU cc_start: 0.7776 (mp) cc_final: 0.7479 (mm) REVERT: A 903 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 1076 MET cc_start: 0.7852 (tpp) cc_final: 0.7428 (tpt) outliers start: 17 outliers final: 10 residues processed: 117 average time/residue: 1.4512 time to fit residues: 180.6286 Evaluate side-chains 116 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 39 optimal weight: 0.0050 chunk 51 optimal weight: 0.8980 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120350 restraints weight = 8432.699| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.77 r_work: 0.3184 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 7749 Z= 0.104 Angle : 0.529 12.527 10562 Z= 0.269 Chirality : 0.041 0.217 1228 Planarity : 0.004 0.046 1304 Dihedral : 8.721 59.595 1315 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.08 % Allowed : 23.44 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 915 helix: 1.99 (0.27), residues: 379 sheet: 0.38 (0.40), residues: 173 loop : 0.31 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 448 HIS 0.014 0.001 HIS A1108 PHE 0.019 0.001 PHE A1141 TYR 0.006 0.001 TYR A1032 ARG 0.007 0.001 ARG A1016 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 341) hydrogen bonds : angle 4.04857 ( 972) SS BOND : bond 0.00736 ( 3) SS BOND : angle 3.60470 ( 6) covalent geometry : bond 0.00245 ( 7746) covalent geometry : angle 0.52252 (10556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6429.00 seconds wall clock time: 114 minutes 56.69 seconds (6896.69 seconds total)