Starting phenix.real_space_refine on Fri Oct 10 16:37:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9q_36995/10_2025/8k9q_36995_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9q_36995/10_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_36995/10_2025/8k9q_36995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9q_36995/10_2025/8k9q_36995.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9q_36995/10_2025/8k9q_36995_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9q_36995/10_2025/8k9q_36995_neut.cif" } resolution = 2.84 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.05, per 1000 atoms: 0.27 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: 0.52 Conformation dependent library (CDL) restraints added in 383.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.23 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: 1.28 Time building geometry restraints manager: 0.75 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: 1.420 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.470 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 468 TYR 0.055 0.004 TYR A 748 PHE 0.030 0.004 PHE A 427 TRP 0.034 0.003 TRP A 448 HIS 0.015 0.002 HIS A 764 Details of bonding type rmsd covalent geometry : bond 0.01492 ( 7746) covalent geometry : angle 1.92091 (10556) SS BOND : bond 0.01893 ( 3) SS BOND : angle 4.50526 ( 6) hydrogen bonds : bond 0.22050 ( 341) hydrogen bonds : angle 8.25849 ( 972) *********************** 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 : 0.260 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: 0.4668 time to fit residues: 108.2830 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 : 0.277 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 249 HIS A 274 ASN A 348 ASN A 391 ASN A 537 HIS A 675 HIS A 677 ASN A 786 GLN A 898 HIS A 900 ASN A1047 ASN A1069 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119993 restraints weight = 8563.741| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.77 r_work: 0.3201 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2530 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= 0.141 Angle : 0.657 8.308 10562 Z= 0.330 Chirality : 0.044 0.199 1228 Planarity : 0.005 0.047 1304 Dihedral : 13.739 97.265 1346 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 5.01 % Allowed : 20.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.27), residues: 915 helix: 1.09 (0.26), residues: 373 sheet: -0.29 (0.38), residues: 163 loop : -0.15 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 198 TYR 0.016 0.001 TYR A 208 PHE 0.017 0.001 PHE A 573 TRP 0.017 0.001 TRP A 448 HIS 0.003 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7746) covalent geometry : angle 0.65265 (10556) SS BOND : bond 0.01647 ( 3) SS BOND : angle 3.15357 ( 6) hydrogen bonds : bond 0.04261 ( 341) hydrogen bonds : angle 4.98923 ( 972) *********************** 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 167 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.242 Fit side-chains REVERT: A 154 LEU cc_start: 0.7974 (tp) cc_final: 0.7723 (tt) REVERT: A 175 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8458 (mtmt) REVERT: A 216 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6414 (t70) REVERT: A 317 ASP cc_start: 0.7823 (m-30) cc_final: 0.7434 (p0) REVERT: A 501 SER cc_start: 0.6659 (t) cc_final: 0.6212 (p) REVERT: A 559 LYS cc_start: 0.7544 (tttm) cc_final: 0.7021 (tptp) REVERT: A 645 LEU cc_start: 0.7293 (tp) cc_final: 0.6829 (tp) REVERT: A 652 GLN cc_start: 0.6839 (mt0) cc_final: 0.6142 (mm-40) REVERT: A 657 ILE cc_start: 0.7788 (mt) cc_final: 0.7530 (mm) REVERT: A 687 ARG cc_start: 0.7481 (mmt180) cc_final: 0.7106 (tpt90) REVERT: A 757 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7616 (mmm160) REVERT: A 790 ASP cc_start: 0.8618 (t70) cc_final: 0.8144 (t0) REVERT: A 870 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7456 (mm) REVERT: A 1076 MET cc_start: 0.7919 (tpp) cc_final: 0.7533 (tpt) outliers start: 41 outliers final: 12 residues processed: 155 average time/residue: 0.4833 time to fit residues: 79.8665 Evaluate side-chains 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 619 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 819 VAL 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 2 optimal weight: 7.9990 chunk 52 optimal weight: 0.0010 chunk 85 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 43 optimal weight: 8.9990 overall best weight: 1.8110 ------------------------------------------------------------------------------- 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 A 899 GLN A 900 ASN A1026 ASN A1071 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115288 restraints weight = 8494.576| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.75 r_work: 0.3115 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7749 Z= 0.177 Angle : 0.632 7.743 10562 Z= 0.317 Chirality : 0.044 0.214 1228 Planarity : 0.005 0.049 1304 Dihedral : 12.687 84.986 1319 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.74 % Allowed : 20.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.28), residues: 915 helix: 1.37 (0.26), residues: 380 sheet: -0.08 (0.39), residues: 165 loop : 0.01 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.012 0.002 TYR A 996 PHE 0.026 0.002 PHE A 826 TRP 0.016 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 7746) covalent geometry : angle 0.62693 (10556) SS BOND : bond 0.00834 ( 3) SS BOND : angle 3.42246 ( 6) hydrogen bonds : bond 0.04391 ( 341) hydrogen bonds : angle 4.78937 ( 972) *********************** 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 166 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.313 Fit side-chains REVERT: A 153 SER cc_start: 0.8764 (t) cc_final: 0.8547 (m) REVERT: A 155 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7949 (tp) REVERT: A 175 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8432 (mtmt) REVERT: A 317 ASP cc_start: 0.7929 (m-30) cc_final: 0.7419 (p0) REVERT: A 471 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7493 (mt0) REVERT: A 559 LYS cc_start: 0.7533 (tttm) cc_final: 0.7060 (tptp) REVERT: A 645 LEU cc_start: 0.7211 (tp) cc_final: 0.6678 (tp) REVERT: A 652 GLN cc_start: 0.6970 (mt0) cc_final: 0.6235 (mm110) REVERT: A 657 ILE cc_start: 0.7824 (mt) cc_final: 0.7545 (mm) REVERT: A 687 ARG cc_start: 0.7370 (mmt180) cc_final: 0.6994 (tpt90) REVERT: A 757 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7647 (mmm160) REVERT: A 790 ASP cc_start: 0.8633 (t70) cc_final: 0.8145 (t0) REVERT: A 794 ASN cc_start: 0.6790 (t0) cc_final: 0.6357 (t0) REVERT: A 863 MET cc_start: 0.8836 (mpp) cc_final: 0.8455 (mmt) REVERT: A 870 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7443 (mm) REVERT: A 993 MET cc_start: 0.5448 (ttt) cc_final: 0.4909 (ttp) REVERT: A 1076 MET cc_start: 0.7907 (tpp) cc_final: 0.7518 (tpt) outliers start: 47 outliers final: 21 residues processed: 150 average time/residue: 0.5282 time to fit residues: 84.2984 Evaluate side-chains 131 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL 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 413 ASP 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 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 802 THR 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 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1056 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 0.0020 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 764 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119377 restraints weight = 8609.368| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.79 r_work: 0.3171 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7749 Z= 0.108 Angle : 0.551 9.006 10562 Z= 0.274 Chirality : 0.042 0.244 1228 Planarity : 0.004 0.047 1304 Dihedral : 11.534 68.225 1318 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.42 % Allowed : 22.95 % Favored : 73.63 % 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 aren not related in a simple way. whole: 1.19 (0.28), residues: 915 helix: 1.83 (0.26), residues: 377 sheet: 0.13 (0.40), residues: 165 loop : 0.12 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 723 TYR 0.008 0.001 TYR A 931 PHE 0.012 0.001 PHE A 573 TRP 0.013 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7746) covalent geometry : angle 0.54524 (10556) SS BOND : bond 0.00518 ( 3) SS BOND : angle 3.34646 ( 6) hydrogen bonds : bond 0.03407 ( 341) hydrogen bonds : angle 4.38089 ( 972) *********************** 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 149 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.302 Fit side-chains REVERT: A 155 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7971 (tp) REVERT: A 175 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8337 (mtmt) REVERT: A 216 ASP cc_start: 0.6893 (m-30) cc_final: 0.6367 (t70) REVERT: A 317 ASP cc_start: 0.7854 (m-30) cc_final: 0.7333 (p0) REVERT: A 462 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: A 501 SER cc_start: 0.6686 (t) cc_final: 0.6455 (p) REVERT: A 559 LYS cc_start: 0.7611 (tttm) cc_final: 0.7068 (tptp) REVERT: A 632 GLU cc_start: 0.7783 (pm20) cc_final: 0.7426 (pm20) REVERT: A 645 LEU cc_start: 0.7140 (tp) cc_final: 0.6651 (tp) REVERT: A 652 GLN cc_start: 0.6904 (mt0) cc_final: 0.6153 (mm110) REVERT: A 657 ILE cc_start: 0.7797 (mt) cc_final: 0.7593 (mm) REVERT: A 687 ARG cc_start: 0.7441 (mmt180) cc_final: 0.6999 (tpt90) REVERT: A 757 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7518 (mmm160) REVERT: A 790 ASP cc_start: 0.8543 (t70) cc_final: 0.8220 (t0) REVERT: A 794 ASN cc_start: 0.6640 (t0) cc_final: 0.6211 (t0) REVERT: A 863 MET cc_start: 0.8820 (mpp) cc_final: 0.8486 (mmt) REVERT: A 870 LEU cc_start: 0.7747 (mp) cc_final: 0.7433 (mm) REVERT: A 1076 MET cc_start: 0.7884 (tpp) cc_final: 0.7514 (tpt) outliers start: 28 outliers final: 12 residues processed: 138 average time/residue: 0.5475 time to fit residues: 80.2672 Evaluate side-chains 119 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 462 ASP 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 859 SER Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 0.0070 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.148054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117169 restraints weight = 8498.583| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.75 r_work: 0.3159 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7749 Z= 0.134 Angle : 0.559 7.786 10562 Z= 0.280 Chirality : 0.042 0.229 1228 Planarity : 0.005 0.049 1304 Dihedral : 10.558 58.808 1316 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.79 % Allowed : 22.95 % Favored : 73.26 % 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 aren not related in a simple way. whole: 1.23 (0.28), residues: 915 helix: 1.84 (0.27), residues: 378 sheet: 0.23 (0.40), residues: 165 loop : 0.13 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1016 TYR 0.010 0.001 TYR A 996 PHE 0.023 0.001 PHE A 826 TRP 0.010 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7746) covalent geometry : angle 0.55121 (10556) SS BOND : bond 0.00849 ( 3) SS BOND : angle 3.95030 ( 6) hydrogen bonds : bond 0.03672 ( 341) hydrogen bonds : angle 4.41935 ( 972) *********************** 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 141 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.315 Fit side-chains REVERT: A 155 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7946 (tp) REVERT: A 175 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8329 (mtmt) REVERT: A 216 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6380 (t70) REVERT: A 310 GLU cc_start: 0.7239 (tt0) cc_final: 0.6821 (tt0) REVERT: A 317 ASP cc_start: 0.7880 (m-30) cc_final: 0.7366 (p0) REVERT: A 501 SER cc_start: 0.6675 (t) cc_final: 0.6380 (p) REVERT: A 559 LYS cc_start: 0.7500 (tttm) cc_final: 0.6996 (tptp) REVERT: A 632 GLU cc_start: 0.7796 (pm20) cc_final: 0.7493 (pm20) REVERT: A 645 LEU cc_start: 0.7150 (tp) cc_final: 0.6670 (tp) REVERT: A 652 GLN cc_start: 0.7037 (mt0) cc_final: 0.6270 (mm110) REVERT: A 656 VAL cc_start: 0.8146 (p) cc_final: 0.7945 (t) REVERT: A 657 ILE cc_start: 0.7752 (mt) cc_final: 0.7548 (mm) REVERT: A 687 ARG cc_start: 0.7458 (mmt180) cc_final: 0.6998 (tpt90) REVERT: A 757 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7574 (mmm160) REVERT: A 790 ASP cc_start: 0.8540 (t70) cc_final: 0.8242 (t0) REVERT: A 794 ASN cc_start: 0.6509 (t0) cc_final: 0.6110 (t0) REVERT: A 809 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8001 (tp) REVERT: A 870 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7525 (mm) REVERT: A 903 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 1076 MET cc_start: 0.7922 (tpp) cc_final: 0.7505 (tpt) outliers start: 31 outliers final: 14 residues processed: 130 average time/residue: 0.5369 time to fit residues: 74.2986 Evaluate side-chains 126 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 629 VAL 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 859 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 906 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 11 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.0470 overall best weight: 1.2882 ------------------------------------------------------------------------------- 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 721 ASN A 898 HIS A1057 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.147853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.116344 restraints weight = 8494.989| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.79 r_work: 0.3154 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7749 Z= 0.139 Angle : 0.552 8.867 10562 Z= 0.278 Chirality : 0.042 0.234 1228 Planarity : 0.005 0.048 1304 Dihedral : 10.230 57.821 1315 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.79 % Allowed : 22.95 % Favored : 73.26 % 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 aren not related in a simple way. whole: 1.19 (0.28), residues: 915 helix: 1.79 (0.26), residues: 378 sheet: 0.26 (0.40), residues: 167 loop : 0.10 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1016 TYR 0.011 0.001 TYR A 996 PHE 0.021 0.001 PHE A 826 TRP 0.008 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7746) covalent geometry : angle 0.54476 (10556) SS BOND : bond 0.00458 ( 3) SS BOND : angle 3.83045 ( 6) hydrogen bonds : bond 0.03669 ( 341) hydrogen bonds : angle 4.34910 ( 972) *********************** 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 140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.294 Fit side-chains REVERT: A 155 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7922 (tp) REVERT: A 175 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8366 (mtmt) REVERT: A 216 ASP cc_start: 0.6991 (m-30) cc_final: 0.6392 (t70) REVERT: A 310 GLU cc_start: 0.7181 (tt0) cc_final: 0.6781 (tt0) REVERT: A 317 ASP cc_start: 0.7903 (m-30) cc_final: 0.7345 (p0) REVERT: A 471 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: A 490 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8892 (mtm) REVERT: A 501 SER cc_start: 0.6637 (t) cc_final: 0.6330 (p) REVERT: A 559 LYS cc_start: 0.7474 (tttm) cc_final: 0.6994 (tptp) REVERT: A 632 GLU cc_start: 0.7813 (pm20) cc_final: 0.7530 (pm20) REVERT: A 645 LEU cc_start: 0.7145 (tp) cc_final: 0.6670 (tp) REVERT: A 652 GLN cc_start: 0.7072 (mt0) cc_final: 0.6288 (mm110) REVERT: A 656 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7920 (t) REVERT: A 657 ILE cc_start: 0.7783 (mt) cc_final: 0.7563 (mm) REVERT: A 687 ARG cc_start: 0.7431 (mmt180) cc_final: 0.6944 (tpt90) REVERT: A 757 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7556 (mmm160) REVERT: A 790 ASP cc_start: 0.8531 (t70) cc_final: 0.8224 (t0) REVERT: A 863 MET cc_start: 0.8803 (mpp) cc_final: 0.8487 (mmt) REVERT: A 870 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7522 (mm) REVERT: A 903 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 912 LEU cc_start: 0.7938 (mt) cc_final: 0.7693 (mm) REVERT: A 1076 MET cc_start: 0.7916 (tpp) cc_final: 0.7488 (tpt) outliers start: 31 outliers final: 14 residues processed: 128 average time/residue: 0.5494 time to fit residues: 74.6601 Evaluate side-chains 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 471 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 799 VAL 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 903 LEU Chi-restraints excluded: chain A residue 906 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.148162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116711 restraints weight = 8522.966| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.79 r_work: 0.3153 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3602 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= 0.133 Angle : 0.552 10.772 10562 Z= 0.278 Chirality : 0.042 0.240 1228 Planarity : 0.004 0.051 1304 Dihedral : 9.991 59.465 1315 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.91 % Allowed : 23.20 % Favored : 72.89 % 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 aren not related in a simple way. whole: 1.23 (0.28), residues: 915 helix: 1.84 (0.26), residues: 377 sheet: 0.25 (0.40), residues: 167 loop : 0.14 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1016 TYR 0.010 0.001 TYR A 996 PHE 0.020 0.001 PHE A 826 TRP 0.009 0.001 TRP A 448 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7746) covalent geometry : angle 0.54283 (10556) SS BOND : bond 0.00574 ( 3) SS BOND : angle 4.13460 ( 6) hydrogen bonds : bond 0.03609 ( 341) hydrogen bonds : angle 4.30269 ( 972) *********************** 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 139 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.305 Fit side-chains REVERT: A 155 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7948 (tp) REVERT: A 175 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8337 (mtmt) REVERT: A 216 ASP cc_start: 0.6922 (m-30) cc_final: 0.6345 (t70) REVERT: A 310 GLU cc_start: 0.7146 (tt0) cc_final: 0.6582 (tt0) REVERT: A 317 ASP cc_start: 0.7927 (m-30) cc_final: 0.7218 (p0) REVERT: A 471 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: A 490 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8897 (mtm) REVERT: A 501 SER cc_start: 0.6669 (t) cc_final: 0.6366 (p) REVERT: A 559 LYS cc_start: 0.7406 (tttm) cc_final: 0.6961 (tptp) REVERT: A 632 GLU cc_start: 0.7843 (pm20) cc_final: 0.7621 (pm20) REVERT: A 645 LEU cc_start: 0.7146 (tp) cc_final: 0.6676 (tp) REVERT: A 652 GLN cc_start: 0.7012 (mt0) cc_final: 0.6337 (mm110) REVERT: A 656 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7936 (t) REVERT: A 657 ILE cc_start: 0.7784 (mt) cc_final: 0.7563 (mm) REVERT: A 687 ARG cc_start: 0.7445 (mmt180) cc_final: 0.6946 (tpt90) REVERT: A 757 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7536 (mmm160) REVERT: A 790 ASP cc_start: 0.8526 (t70) cc_final: 0.8208 (t0) REVERT: A 863 MET cc_start: 0.8799 (mpp) cc_final: 0.8484 (mmt) REVERT: A 870 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7538 (mm) REVERT: A 903 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 912 LEU cc_start: 0.7854 (mt) cc_final: 0.7590 (mm) REVERT: A 1076 MET cc_start: 0.7913 (tpp) cc_final: 0.7485 (tpt) outliers start: 32 outliers final: 14 residues processed: 129 average time/residue: 0.5523 time to fit residues: 75.5725 Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 433 THR 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 523 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 819 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.145561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113976 restraints weight = 8579.673| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.79 r_work: 0.3125 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3559 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= 0.184 Angle : 0.603 12.351 10562 Z= 0.306 Chirality : 0.044 0.259 1228 Planarity : 0.005 0.055 1304 Dihedral : 10.147 59.038 1315 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.91 % Allowed : 23.08 % Favored : 73.02 % 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 aren not related in a simple way. whole: 1.02 (0.28), residues: 915 helix: 1.60 (0.26), residues: 381 sheet: 0.26 (0.41), residues: 165 loop : 0.02 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 630 TYR 0.015 0.002 TYR A 996 PHE 0.027 0.001 PHE A 826 TRP 0.007 0.001 TRP A 448 HIS 0.005 0.001 HIS A1108 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 7746) covalent geometry : angle 0.59505 (10556) SS BOND : bond 0.00943 ( 3) SS BOND : angle 4.21336 ( 6) hydrogen bonds : bond 0.04128 ( 341) hydrogen bonds : angle 4.48068 ( 972) *********************** 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 138 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.286 Fit side-chains REVERT: A 155 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 175 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8360 (mtmt) REVERT: A 310 GLU cc_start: 0.7203 (tt0) cc_final: 0.6573 (tm-30) REVERT: A 317 ASP cc_start: 0.7992 (m-30) cc_final: 0.7230 (p0) REVERT: A 471 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: A 490 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8913 (mtm) REVERT: A 501 SER cc_start: 0.6721 (t) cc_final: 0.6332 (p) REVERT: A 559 LYS cc_start: 0.7484 (tttm) cc_final: 0.7005 (tptp) REVERT: A 632 GLU cc_start: 0.7811 (pm20) cc_final: 0.7519 (pm20) REVERT: A 645 LEU cc_start: 0.7193 (tp) cc_final: 0.6740 (tp) REVERT: A 652 GLN cc_start: 0.7108 (mt0) cc_final: 0.6357 (mm110) REVERT: A 656 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7940 (t) REVERT: A 657 ILE cc_start: 0.7800 (mt) cc_final: 0.7566 (mm) REVERT: A 687 ARG cc_start: 0.7502 (mmt180) cc_final: 0.7034 (tpt90) REVERT: A 757 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7664 (mmm160) REVERT: A 790 ASP cc_start: 0.8553 (t70) cc_final: 0.8281 (t0) REVERT: A 809 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8010 (tp) REVERT: A 863 MET cc_start: 0.8831 (mpp) cc_final: 0.8465 (mmt) REVERT: A 870 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7583 (mm) REVERT: A 903 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8268 (tt) REVERT: A 1076 MET cc_start: 0.7907 (tpp) cc_final: 0.7535 (tpt) outliers start: 32 outliers final: 16 residues processed: 127 average time/residue: 0.5465 time to fit residues: 73.6495 Evaluate side-chains 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 296 ILE 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 509 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 656 VAL 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 819 VAL 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 903 LEU Chi-restraints excluded: chain A residue 952 VAL 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 30 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.148940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117777 restraints weight = 8508.723| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.77 r_work: 0.3173 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3769 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= 0.111 Angle : 0.537 12.983 10562 Z= 0.272 Chirality : 0.041 0.238 1228 Planarity : 0.004 0.052 1304 Dihedral : 9.522 59.057 1315 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.44 % Allowed : 24.42 % Favored : 73.14 % 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 aren not related in a simple way. whole: 1.24 (0.28), residues: 915 helix: 1.79 (0.27), residues: 379 sheet: 0.23 (0.39), residues: 173 loop : 0.20 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1016 TYR 0.007 0.001 TYR A 996 PHE 0.014 0.001 PHE A 826 TRP 0.008 0.001 TRP A 448 HIS 0.008 0.001 HIS A1108 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7746) covalent geometry : angle 0.52991 (10556) SS BOND : bond 0.00530 ( 3) SS BOND : angle 3.68696 ( 6) hydrogen bonds : bond 0.03391 ( 341) hydrogen bonds : angle 4.22180 ( 972) *********************** 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 130 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.301 Fit side-chains REVERT: A 155 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 175 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8324 (mtmt) REVERT: A 216 ASP cc_start: 0.6872 (m-30) cc_final: 0.6295 (t70) REVERT: A 310 GLU cc_start: 0.7174 (tt0) cc_final: 0.6614 (tt0) REVERT: A 317 ASP cc_start: 0.7959 (m-30) cc_final: 0.7212 (p0) REVERT: A 471 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: A 490 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8911 (mtm) REVERT: A 501 SER cc_start: 0.6701 (t) cc_final: 0.6404 (p) REVERT: A 523 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 559 LYS cc_start: 0.7326 (tttm) cc_final: 0.6876 (tptp) REVERT: A 632 GLU cc_start: 0.7845 (pm20) cc_final: 0.7594 (pm20) REVERT: A 645 LEU cc_start: 0.7145 (tp) cc_final: 0.6680 (tp) REVERT: A 652 GLN cc_start: 0.7075 (mt0) cc_final: 0.6345 (mm110) REVERT: A 657 ILE cc_start: 0.7787 (mt) cc_final: 0.7566 (mm) REVERT: A 687 ARG cc_start: 0.7424 (mmt180) cc_final: 0.6977 (tpt90) REVERT: A 757 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7543 (mmm160) REVERT: A 790 ASP cc_start: 0.8503 (t70) cc_final: 0.8203 (t0) REVERT: A 863 MET cc_start: 0.8803 (mpp) cc_final: 0.8489 (mmt) REVERT: A 870 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7510 (mm) REVERT: A 912 LEU cc_start: 0.7747 (mt) cc_final: 0.7513 (mm) REVERT: A 1076 MET cc_start: 0.7896 (tpp) cc_final: 0.7472 (tpt) outliers start: 20 outliers final: 9 residues processed: 121 average time/residue: 0.5751 time to fit residues: 73.7606 Evaluate side-chains 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 509 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 819 VAL 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 1011 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 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 ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117357 restraints weight = 8543.421| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.78 r_work: 0.3145 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7749 Z= 0.117 Angle : 0.539 12.788 10562 Z= 0.273 Chirality : 0.042 0.231 1228 Planarity : 0.004 0.047 1304 Dihedral : 9.338 59.592 1315 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.20 % Allowed : 24.54 % Favored : 73.26 % 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 aren not related in a simple way. whole: 1.27 (0.28), residues: 915 helix: 1.84 (0.27), residues: 379 sheet: 0.22 (0.39), residues: 175 loop : 0.22 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1016 TYR 0.008 0.001 TYR A 996 PHE 0.018 0.001 PHE A 826 TRP 0.009 0.001 TRP A 448 HIS 0.014 0.001 HIS A1108 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7746) covalent geometry : angle 0.53211 (10556) SS BOND : bond 0.00793 ( 3) SS BOND : angle 3.56785 ( 6) hydrogen bonds : bond 0.03426 ( 341) hydrogen bonds : angle 4.19683 ( 972) ********************** 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 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.281 Fit side-chains REVERT: A 155 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7962 (tp) REVERT: A 175 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8321 (mtmt) REVERT: A 216 ASP cc_start: 0.6903 (m-30) cc_final: 0.6288 (t70) REVERT: A 310 GLU cc_start: 0.7127 (tt0) cc_final: 0.6665 (tt0) REVERT: A 317 ASP cc_start: 0.7938 (m-30) cc_final: 0.7190 (p0) REVERT: A 471 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: A 490 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8915 (mtm) REVERT: A 501 SER cc_start: 0.6668 (t) cc_final: 0.6361 (p) REVERT: A 559 LYS cc_start: 0.7360 (tttm) cc_final: 0.6880 (tptp) REVERT: A 632 GLU cc_start: 0.7867 (pm20) cc_final: 0.7656 (pm20) REVERT: A 645 LEU cc_start: 0.7166 (tp) cc_final: 0.6678 (tp) REVERT: A 652 GLN cc_start: 0.7083 (mt0) cc_final: 0.6319 (mm110) REVERT: A 687 ARG cc_start: 0.7445 (mmt180) cc_final: 0.6957 (tpt90) REVERT: A 757 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7551 (mmm160) REVERT: A 790 ASP cc_start: 0.8513 (t70) cc_final: 0.8225 (t0) REVERT: A 863 MET cc_start: 0.8815 (mpp) cc_final: 0.8530 (mmt) REVERT: A 870 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7480 (mm) REVERT: A 912 LEU cc_start: 0.7743 (mt) cc_final: 0.7522 (mm) REVERT: A 1076 MET cc_start: 0.7926 (tpp) cc_final: 0.7514 (tpt) outliers start: 18 outliers final: 10 residues processed: 117 average time/residue: 0.5577 time to fit residues: 69.2706 Evaluate side-chains 119 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 479 MET Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 819 VAL 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 1011 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.149107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117881 restraints weight = 8458.422| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.77 r_work: 0.3174 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7749 Z= 0.114 Angle : 0.536 12.483 10562 Z= 0.271 Chirality : 0.041 0.226 1228 Planarity : 0.004 0.047 1304 Dihedral : 9.162 59.892 1315 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.95 % Allowed : 24.42 % Favored : 73.63 % 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 aren not related in a simple way. whole: 1.32 (0.28), residues: 915 helix: 1.86 (0.27), residues: 379 sheet: 0.26 (0.39), residues: 173 loop : 0.25 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 723 TYR 0.008 0.001 TYR A 996 PHE 0.017 0.001 PHE A 826 TRP 0.009 0.001 TRP A 448 HIS 0.017 0.001 HIS A1108 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7746) covalent geometry : angle 0.52889 (10556) SS BOND : bond 0.00723 ( 3) SS BOND : angle 3.62447 ( 6) hydrogen bonds : bond 0.03360 ( 341) hydrogen bonds : angle 4.14411 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.67 seconds wall clock time: 51 minutes 52.93 seconds (3112.93 seconds total)