Starting phenix.real_space_refine on Mon May 12 00:26:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qju_18449/05_2025/8qju_18449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qju_18449/05_2025/8qju_18449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qju_18449/05_2025/8qju_18449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qju_18449/05_2025/8qju_18449.map" model { file = "/net/cci-nas-00/data/ceres_data/8qju_18449/05_2025/8qju_18449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qju_18449/05_2025/8qju_18449.cif" } resolution = 3.5 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5470 2.51 5 N 1470 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8578 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8578 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 46, 'TRANS': 998} Chain breaks: 4 Time building chain proxies: 5.55, per 1000 atoms: 0.65 Number of scatterers: 8578 At special positions: 0 Unit cell: (85.412, 104.32, 115.404, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1595 8.00 N 1470 7.00 C 5470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 353 " distance=2.07 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: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 34.9% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.768A pdb=" N PHE A 82 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 removed outlier: 3.919A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.558A pdb=" N GLU A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.736A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 222 removed outlier: 3.580A pdb=" N PHE A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N SER A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.539A pdb=" N LEU A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.733A pdb=" N ALA A 308 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.623A pdb=" N ASN A 315 " --> pdb=" O GLN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.976A pdb=" N TYR A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.506A pdb=" N HIS A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 426 removed outlier: 4.005A pdb=" N HIS A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.559A pdb=" N THR A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 639 through 644 removed outlier: 3.835A pdb=" N SER A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 644 " --> pdb=" O PRO A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 644' Processing helix chain 'A' and resid 652 through 663 removed outlier: 3.997A pdb=" N ILE A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 736 through 743 removed outlier: 3.753A pdb=" N ARG A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 removed outlier: 3.624A pdb=" N ASP A 842 " --> pdb=" O GLN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 892 through 908 Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.604A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 Processing helix chain 'A' and resid 970 through 979 removed outlier: 4.660A pdb=" N LEU A 974 " --> pdb=" O LYS A 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1005 Processing helix chain 'A' and resid 1018 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 removed outlier: 3.968A pdb=" N GLY A 63 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 39 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 41 " --> pdb=" O MET A 28 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET A 28 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 110 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 107 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 72 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.665A pdb=" N THR A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 339 " --> pdb=" O THR A 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA6, first strand: chain 'A' and resid 851 through 854 Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565 Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 624 Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.866A pdb=" N ALA A 668 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 680 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 682 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 684 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 691 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 696 " --> pdb=" O VAL A 703 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AB2, first strand: chain 'A' and resid 858 through 862 removed outlier: 3.662A pdb=" N GLU A 877 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 938 through 939 removed outlier: 5.077A pdb=" N LYS A 938 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU A 954 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ARG A 984 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG A 956 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR A 983 " --> pdb=" O MET A1009 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1061 through 1063 removed outlier: 4.292A pdb=" N ARG A1187 " --> pdb=" O THR A1062 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1098 through 1100 removed outlier: 3.997A pdb=" N VAL A1087 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS A1082 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU A1138 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE A1147 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP A1140 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1163 through 1164 300 hydrogen bonds defined for protein. 816 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: 3.00 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1421 1.31 - 1.44: 2389 1.44 - 1.57: 4901 1.57 - 1.70: 0 1.70 - 1.83: 68 Bond restraints: 8779 Sorted by residual: bond pdb=" C THR A1102 " pdb=" O THR A1102 " ideal model delta sigma weight residual 1.234 1.182 0.051 1.17e-02 7.31e+03 1.92e+01 bond pdb=" CA SER A1110 " pdb=" CB SER A1110 " ideal model delta sigma weight residual 1.528 1.487 0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" CA SER A 110 " pdb=" CB SER A 110 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.50e-02 4.44e+03 1.00e+01 bond pdb=" N LEU A1073 " pdb=" CA LEU A1073 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.14e-02 7.69e+03 8.07e+00 bond pdb=" CA SER A1172 " pdb=" CB SER A1172 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.21e-02 6.83e+03 7.25e+00 ... (remaining 8774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 10759 2.42 - 4.83: 990 4.83 - 7.25: 82 7.25 - 9.66: 15 9.66 - 12.08: 3 Bond angle restraints: 11849 Sorted by residual: angle pdb=" N PRO A 400 " pdb=" CA PRO A 400 " pdb=" C PRO A 400 " ideal model delta sigma weight residual 111.32 123.40 -12.08 1.71e+00 3.42e-01 4.99e+01 angle pdb=" N PRO A 75 " pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 113.57 122.36 -8.79 1.31e+00 5.83e-01 4.50e+01 angle pdb=" C PRO A 400 " pdb=" CA PRO A 400 " pdb=" CB PRO A 400 " ideal model delta sigma weight residual 110.85 101.65 9.20 1.41e+00 5.03e-01 4.25e+01 angle pdb=" C PRO A 75 " pdb=" CA PRO A 75 " pdb=" CB PRO A 75 " ideal model delta sigma weight residual 112.11 103.18 8.93 1.46e+00 4.69e-01 3.74e+01 angle pdb=" CA PHE A 505 " pdb=" CB PHE A 505 " pdb=" CG PHE A 505 " ideal model delta sigma weight residual 113.80 119.26 -5.46 1.00e+00 1.00e+00 2.98e+01 ... (remaining 11844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4702 17.12 - 34.23: 442 34.23 - 51.34: 96 51.34 - 68.46: 88 68.46 - 85.57: 2 Dihedral angle restraints: 5330 sinusoidal: 2245 harmonic: 3085 Sorted by residual: dihedral pdb=" CB CYS A 348 " pdb=" SG CYS A 348 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual 93.00 153.46 -60.46 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CA ALA A 259 " pdb=" C ALA A 259 " pdb=" N GLN A 260 " pdb=" CA GLN A 260 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR A 706 " pdb=" C THR A 706 " pdb=" N SER A 707 " pdb=" CA SER A 707 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 5327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 902 0.083 - 0.166: 332 0.166 - 0.249: 34 0.249 - 0.332: 4 0.332 - 0.415: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CA PHE A1028 " pdb=" N PHE A1028 " pdb=" C PHE A1028 " pdb=" CB PHE A1028 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TYR A1020 " pdb=" N TYR A1020 " pdb=" C TYR A1020 " pdb=" CB TYR A1020 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ARG A 248 " pdb=" N ARG A 248 " pdb=" C ARG A 248 " pdb=" CB ARG A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1270 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 679 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C SER A 679 " 0.054 2.00e-02 2.50e+03 pdb=" O SER A 679 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 680 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 147 " -0.260 9.50e-02 1.11e+02 1.17e-01 8.71e+00 pdb=" NE ARG A 147 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 147 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 147 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 147 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1153 " 0.039 2.00e-02 2.50e+03 2.01e-02 8.05e+00 pdb=" CG TYR A1153 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A1153 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A1153 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A1153 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A1153 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A1153 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A1153 " 0.022 2.00e-02 2.50e+03 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1683 2.77 - 3.31: 8974 3.31 - 3.84: 13878 3.84 - 4.37: 16841 4.37 - 4.90: 27064 Nonbonded interactions: 68440 Sorted by model distance: nonbonded pdb=" OH TYR A 647 " pdb=" NZ LYS A 673 " model vdw 2.243 3.120 nonbonded pdb=" O PRO A 400 " pdb=" OH TYR A1036 " model vdw 2.245 3.040 nonbonded pdb=" O THR A 332 " pdb=" OG SER A 338 " model vdw 2.248 3.040 nonbonded pdb=" O ARG A 700 " pdb=" ND1 HIS A 701 " model vdw 2.261 3.120 nonbonded pdb=" O GLU A 279 " pdb=" OG1 THR A 280 " model vdw 2.285 3.040 ... (remaining 68435 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.940 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.007 0.051 8780 Z= 0.500 Angle : 1.446 12.078 11851 Z= 0.979 Chirality : 0.078 0.415 1273 Planarity : 0.010 0.117 1521 Dihedral : 16.446 85.571 3323 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 31.96 Ramachandran Plot: Outliers : 2.13 % Allowed : 8.79 % Favored : 89.08 % Rotamer: Outliers : 10.42 % Allowed : 12.21 % Favored : 77.37 % Cbeta Deviations : 0.10 % 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: -2.58 (0.23), residues: 1035 helix: -1.69 (0.25), residues: 284 sheet: -1.34 (0.37), residues: 198 loop : -1.84 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP A 322 HIS 0.008 0.002 HIS A 252 PHE 0.036 0.004 PHE A 505 TYR 0.039 0.006 TYR A1153 ARG 0.018 0.002 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.26608 ( 298) hydrogen bonds : angle 9.82690 ( 816) SS BOND : bond 0.03762 ( 1) SS BOND : angle 2.00407 ( 2) covalent geometry : bond 0.00732 ( 8779) covalent geometry : angle 1.44624 (11849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 302 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8445 (tp40) cc_final: 0.7998 (tm-30) REVERT: A 20 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.7910 (tmm-80) REVERT: A 28 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8139 (mtp) REVERT: A 68 MET cc_start: 0.8701 (mmm) cc_final: 0.8441 (mtt) REVERT: A 93 ASP cc_start: 0.8354 (t0) cc_final: 0.7788 (p0) REVERT: A 164 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8926 (ttm110) REVERT: A 186 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5787 (mmtp) REVERT: A 196 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: A 200 GLU cc_start: 0.9032 (mp0) cc_final: 0.8692 (tp30) REVERT: A 249 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8298 (t80) REVERT: A 289 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: A 314 MET cc_start: 0.8018 (mmm) cc_final: 0.7160 (mmm) REVERT: A 320 HIS cc_start: 0.8230 (m90) cc_final: 0.7656 (m-70) REVERT: A 409 CYS cc_start: 0.8826 (m) cc_final: 0.8431 (m) REVERT: A 484 TRP cc_start: 0.7483 (t-100) cc_final: 0.7224 (t-100) REVERT: A 592 MET cc_start: -0.3752 (mtt) cc_final: -0.3980 (pmm) REVERT: A 646 TRP cc_start: 0.8388 (p-90) cc_final: 0.7670 (p-90) REVERT: A 651 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8762 (tp) REVERT: A 652 SER cc_start: 0.8620 (t) cc_final: 0.8225 (p) REVERT: A 693 CYS cc_start: 0.8484 (t) cc_final: 0.8098 (p) REVERT: A 728 LYS cc_start: 0.9237 (mptm) cc_final: 0.8857 (tmtt) REVERT: A 729 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.9018 (ppp) REVERT: A 859 ASN cc_start: 0.8504 (m-40) cc_final: 0.8278 (p0) REVERT: A 868 ASN cc_start: 0.8457 (m-40) cc_final: 0.8117 (m-40) REVERT: A 873 VAL cc_start: 0.9324 (p) cc_final: 0.9105 (t) REVERT: A 886 VAL cc_start: 0.8619 (t) cc_final: 0.8394 (m) REVERT: A 938 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7882 (ttmm) REVERT: A 953 ARG cc_start: 0.8846 (ptp-110) cc_final: 0.8504 (mtm-85) REVERT: A 970 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.4597 (pptt) REVERT: A 997 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7773 (p90) REVERT: A 1039 GLN cc_start: 0.8916 (mt0) cc_final: 0.8674 (mt0) REVERT: A 1051 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8999 (mmm) REVERT: A 1110 SER cc_start: 0.9044 (p) cc_final: 0.8843 (t) REVERT: A 1141 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8746 (mtm) REVERT: A 1164 SER cc_start: 0.8829 (t) cc_final: 0.8407 (p) REVERT: A 1176 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 1186 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.9009 (mtm) outliers start: 99 outliers final: 42 residues processed: 361 average time/residue: 0.2353 time to fit residues: 113.7977 Evaluate side-chains 279 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 636 PRO Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 680 TYR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 997 TYR Chi-restraints excluded: chain A residue 1014 PHE Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1025 HIS Chi-restraints excluded: chain A residue 1051 MET Chi-restraints excluded: chain A residue 1096 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1186 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 121 ASN A 201 GLN A 247 GLN A 260 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 HIS A 387 GLN A 413 GLN A 446 GLN A 616 HIS A 637 ASN A 856 ASN A 868 ASN A 979 GLN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1031 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.133330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100208 restraints weight = 14340.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104090 restraints weight = 6723.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106655 restraints weight = 4098.824| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8780 Z= 0.171 Angle : 0.748 9.042 11851 Z= 0.405 Chirality : 0.046 0.224 1273 Planarity : 0.006 0.105 1521 Dihedral : 10.875 61.741 1262 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.18 % Favored : 93.24 % Rotamer: Outliers : 6.53 % Allowed : 17.26 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.14 (0.25), residues: 1035 helix: 0.68 (0.28), residues: 311 sheet: -0.91 (0.36), residues: 209 loop : -1.60 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 54 HIS 0.006 0.001 HIS A 641 PHE 0.019 0.002 PHE A 272 TYR 0.018 0.002 TYR A1137 ARG 0.008 0.001 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 298) hydrogen bonds : angle 5.78332 ( 816) SS BOND : bond 0.00083 ( 1) SS BOND : angle 1.38361 ( 2) covalent geometry : bond 0.00370 ( 8779) covalent geometry : angle 0.74820 (11849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7804 (tp40) cc_final: 0.7355 (tm-30) REVERT: A 20 ARG cc_start: 0.8002 (tpp-160) cc_final: 0.7351 (tmm-80) REVERT: A 28 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7665 (ptp) REVERT: A 214 GLN cc_start: 0.8190 (mt0) cc_final: 0.7717 (mt0) REVERT: A 314 MET cc_start: 0.7733 (mmm) cc_final: 0.6697 (mmt) REVERT: A 320 HIS cc_start: 0.7771 (m90) cc_final: 0.7022 (m-70) REVERT: A 355 CYS cc_start: 0.7308 (t) cc_final: 0.6774 (t) REVERT: A 449 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7381 (tt0) REVERT: A 477 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7560 (tp-100) REVERT: A 548 GLN cc_start: 0.8804 (pt0) cc_final: 0.8479 (pm20) REVERT: A 646 TRP cc_start: 0.7895 (p-90) cc_final: 0.7249 (p-90) REVERT: A 651 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8416 (tp) REVERT: A 658 ASP cc_start: 0.8889 (m-30) cc_final: 0.8513 (m-30) REVERT: A 843 ASN cc_start: 0.7969 (m-40) cc_final: 0.7754 (m-40) REVERT: A 859 ASN cc_start: 0.7639 (m-40) cc_final: 0.7427 (p0) REVERT: A 873 VAL cc_start: 0.9314 (p) cc_final: 0.9037 (t) REVERT: A 886 VAL cc_start: 0.8085 (t) cc_final: 0.7831 (m) REVERT: A 895 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 897 PHE cc_start: 0.8563 (t80) cc_final: 0.8232 (t80) REVERT: A 898 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8375 (mt-10) REVERT: A 930 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 946 ASN cc_start: 0.7905 (t0) cc_final: 0.7530 (t0) REVERT: A 960 GLU cc_start: 0.7434 (pt0) cc_final: 0.6978 (pt0) REVERT: A 964 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7919 (t0) REVERT: A 978 ASN cc_start: 0.8111 (m-40) cc_final: 0.7463 (t0) REVERT: A 996 ASN cc_start: 0.8441 (m-40) cc_final: 0.7996 (m-40) REVERT: A 1009 MET cc_start: 0.7441 (mtt) cc_final: 0.6965 (mtt) REVERT: A 1039 GLN cc_start: 0.8415 (mt0) cc_final: 0.8117 (mt0) REVERT: A 1045 THR cc_start: 0.7587 (p) cc_final: 0.7353 (p) REVERT: A 1061 MET cc_start: 0.7175 (mtt) cc_final: 0.6716 (ttt) REVERT: A 1105 ASN cc_start: 0.8182 (t0) cc_final: 0.7941 (m-40) REVERT: A 1110 SER cc_start: 0.8456 (p) cc_final: 0.8225 (t) REVERT: A 1152 THR cc_start: 0.8670 (m) cc_final: 0.8318 (p) REVERT: A 1186 MET cc_start: 0.7853 (mtm) cc_final: 0.7465 (mtm) outliers start: 62 outliers final: 27 residues processed: 270 average time/residue: 0.1972 time to fit residues: 72.9808 Evaluate side-chains 227 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1096 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 0.0370 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS A 868 ASN ** A1025 HIS ** 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 = 0.3875 r_free = 0.3875 target = 0.135064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101410 restraints weight = 14222.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105501 restraints weight = 6513.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108127 restraints weight = 3903.105| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8780 Z= 0.157 Angle : 0.670 8.832 11851 Z= 0.355 Chirality : 0.043 0.314 1273 Planarity : 0.005 0.042 1521 Dihedral : 8.606 58.955 1189 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.86 % Favored : 92.66 % Rotamer: Outliers : 5.16 % Allowed : 20.00 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -0.66 (0.26), residues: 1035 helix: 1.48 (0.29), residues: 305 sheet: -0.75 (0.36), residues: 218 loop : -1.51 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 54 HIS 0.013 0.001 HIS A 327 PHE 0.025 0.002 PHE A 272 TYR 0.013 0.001 TYR A1094 ARG 0.008 0.001 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 298) hydrogen bonds : angle 5.18978 ( 816) SS BOND : bond 0.00388 ( 1) SS BOND : angle 1.22050 ( 2) covalent geometry : bond 0.00356 ( 8779) covalent geometry : angle 0.67004 (11849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7770 (tp40) cc_final: 0.7300 (tm-30) REVERT: A 20 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7229 (tmm-80) REVERT: A 41 ARG cc_start: 0.8198 (mmt90) cc_final: 0.7957 (mmt90) REVERT: A 109 LEU cc_start: 0.8300 (tp) cc_final: 0.8082 (tt) REVERT: A 164 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7414 (ttp80) REVERT: A 235 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7870 (ptp90) REVERT: A 320 HIS cc_start: 0.7915 (m90) cc_final: 0.7400 (m-70) REVERT: A 354 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.3911 (mmp-170) REVERT: A 355 CYS cc_start: 0.7267 (t) cc_final: 0.6621 (t) REVERT: A 359 ASP cc_start: 0.6232 (m-30) cc_final: 0.5567 (m-30) REVERT: A 379 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7304 (mmtt) REVERT: A 423 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 449 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7635 (tt0) REVERT: A 477 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7654 (tp-100) REVERT: A 485 ASP cc_start: 0.5618 (OUTLIER) cc_final: 0.4908 (t0) REVERT: A 548 GLN cc_start: 0.8933 (pt0) cc_final: 0.8518 (pm20) REVERT: A 651 LEU cc_start: 0.8503 (tp) cc_final: 0.8296 (tp) REVERT: A 658 ASP cc_start: 0.8939 (m-30) cc_final: 0.8512 (m-30) REVERT: A 843 ASN cc_start: 0.8100 (m-40) cc_final: 0.7773 (m-40) REVERT: A 886 VAL cc_start: 0.7958 (t) cc_final: 0.7675 (m) REVERT: A 895 GLU cc_start: 0.8112 (mp0) cc_final: 0.7387 (mp0) REVERT: A 897 PHE cc_start: 0.8765 (t80) cc_final: 0.8435 (t80) REVERT: A 901 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8419 (mm110) REVERT: A 946 ASN cc_start: 0.8003 (t0) cc_final: 0.7589 (t0) REVERT: A 951 ASP cc_start: 0.7798 (t0) cc_final: 0.7058 (t0) REVERT: A 960 GLU cc_start: 0.7615 (pt0) cc_final: 0.7046 (pt0) REVERT: A 964 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7999 (t0) REVERT: A 978 ASN cc_start: 0.8120 (m-40) cc_final: 0.7453 (t0) REVERT: A 996 ASN cc_start: 0.8311 (m-40) cc_final: 0.8061 (m-40) REVERT: A 1004 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 1009 MET cc_start: 0.7384 (mtt) cc_final: 0.6834 (mtt) REVERT: A 1045 THR cc_start: 0.7733 (p) cc_final: 0.7478 (p) REVERT: A 1048 TYR cc_start: 0.8087 (t80) cc_final: 0.7789 (t80) REVERT: A 1051 MET cc_start: 0.8857 (mmm) cc_final: 0.8572 (mmm) REVERT: A 1061 MET cc_start: 0.7112 (mtt) cc_final: 0.6857 (ttt) REVERT: A 1110 SER cc_start: 0.8541 (p) cc_final: 0.8339 (t) outliers start: 49 outliers final: 31 residues processed: 238 average time/residue: 0.2022 time to fit residues: 66.7001 Evaluate side-chains 215 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1096 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1182 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN A 527 HIS A 843 ASN A 868 ASN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.131545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098031 restraints weight = 14143.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101879 restraints weight = 6627.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104471 restraints weight = 4038.090| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8780 Z= 0.232 Angle : 0.687 9.459 11851 Z= 0.363 Chirality : 0.044 0.221 1273 Planarity : 0.005 0.045 1521 Dihedral : 8.121 59.959 1175 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.73 % Favored : 91.79 % Rotamer: Outliers : 5.89 % Allowed : 20.95 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -0.81 (0.26), residues: 1035 helix: 1.44 (0.29), residues: 305 sheet: -0.84 (0.34), residues: 229 loop : -1.68 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 54 HIS 0.006 0.001 HIS A 327 PHE 0.037 0.002 PHE A 272 TYR 0.017 0.002 TYR A 986 ARG 0.010 0.001 ARG A 700 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 298) hydrogen bonds : angle 5.14896 ( 816) SS BOND : bond 0.00449 ( 1) SS BOND : angle 1.11831 ( 2) covalent geometry : bond 0.00542 ( 8779) covalent geometry : angle 0.68655 (11849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7777 (tp40) cc_final: 0.7356 (tm-30) REVERT: A 20 ARG cc_start: 0.8041 (tpp-160) cc_final: 0.7326 (tmm-80) REVERT: A 210 MET cc_start: 0.8272 (mmm) cc_final: 0.7223 (mmm) REVERT: A 214 GLN cc_start: 0.8203 (mt0) cc_final: 0.7952 (mt0) REVERT: A 354 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.4299 (mmp-170) REVERT: A 361 TRP cc_start: 0.8207 (m100) cc_final: 0.7689 (m100) REVERT: A 421 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7038 (t80) REVERT: A 477 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7687 (tp-100) REVERT: A 548 GLN cc_start: 0.8993 (pt0) cc_final: 0.8533 (pm20) REVERT: A 651 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8299 (tp) REVERT: A 658 ASP cc_start: 0.8926 (m-30) cc_final: 0.8481 (m-30) REVERT: A 690 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7541 (p) REVERT: A 843 ASN cc_start: 0.8193 (m110) cc_final: 0.7836 (m110) REVERT: A 886 VAL cc_start: 0.8037 (t) cc_final: 0.7807 (m) REVERT: A 897 PHE cc_start: 0.8649 (t80) cc_final: 0.8438 (t80) REVERT: A 946 ASN cc_start: 0.7984 (t0) cc_final: 0.7577 (t0) REVERT: A 964 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7944 (t0) REVERT: A 978 ASN cc_start: 0.8153 (m-40) cc_final: 0.7505 (t0) REVERT: A 997 TYR cc_start: 0.8296 (p90) cc_final: 0.7879 (p90) REVERT: A 1004 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8992 (tt) REVERT: A 1045 THR cc_start: 0.8049 (p) cc_final: 0.7761 (p) REVERT: A 1051 MET cc_start: 0.8912 (mmm) cc_final: 0.8618 (mmm) REVERT: A 1057 ARG cc_start: 0.6395 (mtm-85) cc_final: 0.6031 (ptp-170) REVERT: A 1087 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7607 (m) REVERT: A 1152 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8325 (p) outliers start: 56 outliers final: 33 residues processed: 230 average time/residue: 0.1991 time to fit residues: 63.4700 Evaluate side-chains 217 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1090 CYS Chi-restraints excluded: chain A residue 1096 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1152 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 0.0770 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A1025 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100331 restraints weight = 14050.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104338 restraints weight = 6481.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106959 restraints weight = 3910.198| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8780 Z= 0.147 Angle : 0.628 9.387 11851 Z= 0.332 Chirality : 0.043 0.289 1273 Planarity : 0.004 0.051 1521 Dihedral : 7.712 59.046 1172 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.44 % Favored : 92.17 % Rotamer: Outliers : 4.95 % Allowed : 22.32 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -0.60 (0.26), residues: 1035 helix: 1.69 (0.30), residues: 303 sheet: -0.70 (0.35), residues: 227 loop : -1.60 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 258 HIS 0.005 0.001 HIS A 327 PHE 0.039 0.002 PHE A 272 TYR 0.026 0.001 TYR A 371 ARG 0.006 0.001 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 298) hydrogen bonds : angle 4.88775 ( 816) SS BOND : bond 0.00301 ( 1) SS BOND : angle 1.15790 ( 2) covalent geometry : bond 0.00335 ( 8779) covalent geometry : angle 0.62760 (11849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7701 (tp40) cc_final: 0.7396 (tm-30) REVERT: A 20 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7291 (tmm-80) REVERT: A 57 THR cc_start: 0.8585 (t) cc_final: 0.8263 (p) REVERT: A 64 PHE cc_start: 0.7768 (p90) cc_final: 0.7534 (p90) REVERT: A 154 ASP cc_start: 0.7083 (t0) cc_final: 0.6735 (t0) REVERT: A 160 SER cc_start: 0.8318 (m) cc_final: 0.7810 (p) REVERT: A 210 MET cc_start: 0.8242 (mmm) cc_final: 0.7304 (mmm) REVERT: A 214 GLN cc_start: 0.7989 (mt0) cc_final: 0.7665 (mt0) REVERT: A 354 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.4127 (mmp-170) REVERT: A 359 ASP cc_start: 0.6273 (m-30) cc_final: 0.5882 (m-30) REVERT: A 379 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7725 (mmtp) REVERT: A 421 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7095 (t80) REVERT: A 423 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 477 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7612 (tp-100) REVERT: A 548 GLN cc_start: 0.9037 (pt0) cc_final: 0.8532 (pm20) REVERT: A 651 LEU cc_start: 0.8442 (tp) cc_final: 0.8223 (tp) REVERT: A 658 ASP cc_start: 0.8914 (m-30) cc_final: 0.8456 (m-30) REVERT: A 690 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7532 (p) REVERT: A 843 ASN cc_start: 0.8190 (m110) cc_final: 0.7819 (m110) REVERT: A 868 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.6791 (t0) REVERT: A 886 VAL cc_start: 0.7988 (t) cc_final: 0.7734 (m) REVERT: A 897 PHE cc_start: 0.8638 (t80) cc_final: 0.8126 (t80) REVERT: A 901 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8494 (mm-40) REVERT: A 946 ASN cc_start: 0.7923 (t0) cc_final: 0.7510 (t0) REVERT: A 964 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7904 (t0) REVERT: A 978 ASN cc_start: 0.8166 (m-40) cc_final: 0.7560 (t0) REVERT: A 996 ASN cc_start: 0.8235 (m-40) cc_final: 0.7983 (m-40) REVERT: A 997 TYR cc_start: 0.8161 (p90) cc_final: 0.7667 (p90) REVERT: A 1009 MET cc_start: 0.7276 (mtt) cc_final: 0.7065 (mtt) REVERT: A 1039 GLN cc_start: 0.8692 (mt0) cc_final: 0.8331 (mt0) REVERT: A 1045 THR cc_start: 0.8116 (p) cc_final: 0.7824 (p) REVERT: A 1051 MET cc_start: 0.8920 (mmm) cc_final: 0.8622 (mmm) REVERT: A 1152 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 1186 MET cc_start: 0.7966 (mtm) cc_final: 0.7697 (mtm) outliers start: 47 outliers final: 35 residues processed: 221 average time/residue: 0.1946 time to fit residues: 60.6689 Evaluate side-chains 221 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1096 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 GLU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 20.0000 chunk 90 optimal weight: 0.0050 chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.128634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095311 restraints weight = 14437.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099142 restraints weight = 6752.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101705 restraints weight = 4115.624| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8780 Z= 0.223 Angle : 0.668 9.228 11851 Z= 0.352 Chirality : 0.043 0.242 1273 Planarity : 0.005 0.064 1521 Dihedral : 7.748 58.220 1172 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.99 % Favored : 90.63 % Rotamer: Outliers : 6.21 % Allowed : 21.79 % Favored : 72.00 % 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: -0.76 (0.26), residues: 1035 helix: 1.54 (0.30), residues: 304 sheet: -0.75 (0.35), residues: 229 loop : -1.72 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 258 HIS 0.004 0.001 HIS A 392 PHE 0.043 0.002 PHE A 272 TYR 0.035 0.002 TYR A 371 ARG 0.007 0.001 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 298) hydrogen bonds : angle 5.00736 ( 816) SS BOND : bond 0.00382 ( 1) SS BOND : angle 1.09416 ( 2) covalent geometry : bond 0.00521 ( 8779) covalent geometry : angle 0.66807 (11849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8025 (tpp-160) cc_final: 0.7284 (tmm-80) REVERT: A 57 THR cc_start: 0.8634 (t) cc_final: 0.8301 (p) REVERT: A 64 PHE cc_start: 0.7901 (p90) cc_final: 0.7654 (p90) REVERT: A 127 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7904 (ttmt) REVERT: A 154 ASP cc_start: 0.7224 (t0) cc_final: 0.6763 (t0) REVERT: A 160 SER cc_start: 0.8307 (m) cc_final: 0.7947 (p) REVERT: A 190 ILE cc_start: 0.8365 (mp) cc_final: 0.8082 (mp) REVERT: A 210 MET cc_start: 0.8253 (mmm) cc_final: 0.7291 (mmm) REVERT: A 214 GLN cc_start: 0.8170 (mt0) cc_final: 0.7899 (mt0) REVERT: A 354 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.4325 (mmp-170) REVERT: A 359 ASP cc_start: 0.6625 (m-30) cc_final: 0.6313 (m-30) REVERT: A 361 TRP cc_start: 0.8136 (m100) cc_final: 0.7647 (m100) REVERT: A 379 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7823 (mmtp) REVERT: A 423 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 477 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7792 (tp-100) REVERT: A 487 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8390 (mt) REVERT: A 651 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8197 (tp) REVERT: A 658 ASP cc_start: 0.8937 (m-30) cc_final: 0.8488 (m-30) REVERT: A 690 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7510 (p) REVERT: A 843 ASN cc_start: 0.8253 (m110) cc_final: 0.7838 (m110) REVERT: A 886 VAL cc_start: 0.7956 (t) cc_final: 0.7676 (m) REVERT: A 897 PHE cc_start: 0.8689 (t80) cc_final: 0.8177 (t80) REVERT: A 901 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8551 (mm-40) REVERT: A 946 ASN cc_start: 0.7996 (t0) cc_final: 0.7465 (t0) REVERT: A 978 ASN cc_start: 0.8170 (m-40) cc_final: 0.7500 (t0) REVERT: A 1009 MET cc_start: 0.7544 (mtt) cc_final: 0.7329 (mtt) REVERT: A 1045 THR cc_start: 0.8194 (p) cc_final: 0.7914 (p) REVERT: A 1048 TYR cc_start: 0.8041 (t80) cc_final: 0.7818 (t80) REVERT: A 1051 MET cc_start: 0.8918 (mmm) cc_final: 0.8618 (mmm) REVERT: A 1057 ARG cc_start: 0.6337 (ptp-170) cc_final: 0.5421 (ptp-170) REVERT: A 1061 MET cc_start: 0.6946 (ttt) cc_final: 0.6707 (ttt) REVERT: A 1152 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 1186 MET cc_start: 0.8086 (mtm) cc_final: 0.7831 (mtm) outliers start: 59 outliers final: 39 residues processed: 220 average time/residue: 0.1762 time to fit residues: 55.4659 Evaluate side-chains 225 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 GLU Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098644 restraints weight = 14372.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102625 restraints weight = 6689.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105256 restraints weight = 4063.373| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8780 Z= 0.132 Angle : 0.627 9.212 11851 Z= 0.327 Chirality : 0.042 0.246 1273 Planarity : 0.004 0.049 1521 Dihedral : 7.334 58.861 1170 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.83 % Favored : 91.79 % Rotamer: Outliers : 4.42 % Allowed : 24.00 % Favored : 71.58 % 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: -0.56 (0.26), residues: 1035 helix: 1.68 (0.30), residues: 304 sheet: -0.58 (0.37), residues: 209 loop : -1.58 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 258 HIS 0.004 0.001 HIS A 392 PHE 0.023 0.002 PHE A 900 TYR 0.031 0.001 TYR A 371 ARG 0.005 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 298) hydrogen bonds : angle 4.75808 ( 816) SS BOND : bond 0.00184 ( 1) SS BOND : angle 1.09141 ( 2) covalent geometry : bond 0.00298 ( 8779) covalent geometry : angle 0.62711 (11849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7691 (tp40) cc_final: 0.7395 (tm-30) REVERT: A 20 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.7254 (tmm-80) REVERT: A 64 PHE cc_start: 0.7789 (p90) cc_final: 0.7566 (p90) REVERT: A 135 ASN cc_start: 0.8527 (t0) cc_final: 0.7563 (p0) REVERT: A 154 ASP cc_start: 0.7289 (t0) cc_final: 0.7070 (t0) REVERT: A 160 SER cc_start: 0.8239 (m) cc_final: 0.7862 (p) REVERT: A 190 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 210 MET cc_start: 0.8205 (mmm) cc_final: 0.7332 (mmm) REVERT: A 214 GLN cc_start: 0.7974 (mt0) cc_final: 0.7678 (mt0) REVERT: A 320 HIS cc_start: 0.8076 (m90) cc_final: 0.7374 (m-70) REVERT: A 354 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.4024 (mmp-170) REVERT: A 359 ASP cc_start: 0.6072 (m-30) cc_final: 0.5677 (m-30) REVERT: A 405 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 423 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 477 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7694 (tp-100) REVERT: A 487 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 548 GLN cc_start: 0.9098 (pt0) cc_final: 0.8624 (pm20) REVERT: A 651 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8145 (tp) REVERT: A 658 ASP cc_start: 0.8927 (m-30) cc_final: 0.8447 (m-30) REVERT: A 700 ARG cc_start: 0.9186 (ttp80) cc_final: 0.8902 (ttp80) REVERT: A 843 ASN cc_start: 0.8246 (m110) cc_final: 0.7809 (m110) REVERT: A 886 VAL cc_start: 0.7925 (t) cc_final: 0.7624 (m) REVERT: A 897 PHE cc_start: 0.8687 (t80) cc_final: 0.8213 (t80) REVERT: A 901 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8511 (mm-40) REVERT: A 946 ASN cc_start: 0.7919 (t0) cc_final: 0.7385 (t0) REVERT: A 978 ASN cc_start: 0.8084 (m-40) cc_final: 0.7496 (t0) REVERT: A 997 TYR cc_start: 0.8122 (p90) cc_final: 0.7562 (p90) REVERT: A 1045 THR cc_start: 0.8158 (p) cc_final: 0.7878 (p) REVERT: A 1051 MET cc_start: 0.8969 (mmm) cc_final: 0.8689 (mmm) REVERT: A 1057 ARG cc_start: 0.6458 (ptp-170) cc_final: 0.6256 (mtm-85) REVERT: A 1152 THR cc_start: 0.8579 (m) cc_final: 0.8325 (p) REVERT: A 1186 MET cc_start: 0.8031 (mtm) cc_final: 0.7625 (mtm) outliers start: 42 outliers final: 29 residues processed: 221 average time/residue: 0.1952 time to fit residues: 60.3924 Evaluate side-chains 213 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1123 GLU Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100581 restraints weight = 14182.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104581 restraints weight = 6552.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107288 restraints weight = 3952.716| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8780 Z= 0.146 Angle : 0.629 7.308 11851 Z= 0.329 Chirality : 0.042 0.237 1273 Planarity : 0.004 0.046 1521 Dihedral : 6.911 58.944 1164 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.02 % Favored : 91.59 % Rotamer: Outliers : 4.00 % Allowed : 24.53 % Favored : 71.47 % 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: -0.51 (0.26), residues: 1035 helix: 1.68 (0.30), residues: 306 sheet: -0.60 (0.37), residues: 212 loop : -1.51 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 258 HIS 0.004 0.001 HIS A 392 PHE 0.029 0.002 PHE A 272 TYR 0.026 0.001 TYR A 371 ARG 0.008 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 298) hydrogen bonds : angle 4.71829 ( 816) SS BOND : bond 0.00197 ( 1) SS BOND : angle 1.03080 ( 2) covalent geometry : bond 0.00339 ( 8779) covalent geometry : angle 0.62922 (11849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7675 (tp40) cc_final: 0.7390 (tm-30) REVERT: A 20 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7250 (tmm-80) REVERT: A 64 PHE cc_start: 0.7806 (p90) cc_final: 0.7567 (p90) REVERT: A 127 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7872 (ttmt) REVERT: A 135 ASN cc_start: 0.8542 (t0) cc_final: 0.7572 (p0) REVERT: A 154 ASP cc_start: 0.7311 (t0) cc_final: 0.7090 (t0) REVERT: A 160 SER cc_start: 0.8226 (m) cc_final: 0.7912 (p) REVERT: A 190 ILE cc_start: 0.8334 (mp) cc_final: 0.8065 (mp) REVERT: A 210 MET cc_start: 0.8220 (mmm) cc_final: 0.7277 (mmm) REVERT: A 214 GLN cc_start: 0.7994 (mt0) cc_final: 0.7701 (mt0) REVERT: A 320 HIS cc_start: 0.8077 (m90) cc_final: 0.7364 (m-70) REVERT: A 354 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.3848 (mmp-170) REVERT: A 359 ASP cc_start: 0.6043 (m-30) cc_final: 0.5662 (m-30) REVERT: A 405 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8298 (mt) REVERT: A 423 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 432 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8824 (mtpp) REVERT: A 477 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7759 (tp-100) REVERT: A 487 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8300 (mt) REVERT: A 548 GLN cc_start: 0.9114 (pt0) cc_final: 0.8658 (pm20) REVERT: A 651 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 658 ASP cc_start: 0.8940 (m-30) cc_final: 0.8450 (m-30) REVERT: A 700 ARG cc_start: 0.9145 (ttp80) cc_final: 0.8860 (ttp80) REVERT: A 843 ASN cc_start: 0.8231 (m110) cc_final: 0.7782 (m110) REVERT: A 886 VAL cc_start: 0.7912 (t) cc_final: 0.7595 (m) REVERT: A 897 PHE cc_start: 0.8693 (t80) cc_final: 0.8224 (t80) REVERT: A 901 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8513 (mm-40) REVERT: A 978 ASN cc_start: 0.8065 (m-40) cc_final: 0.7511 (t0) REVERT: A 997 TYR cc_start: 0.8109 (p90) cc_final: 0.7544 (p90) REVERT: A 1009 MET cc_start: 0.7229 (mtt) cc_final: 0.6741 (mtt) REVERT: A 1045 THR cc_start: 0.8160 (p) cc_final: 0.7875 (p) REVERT: A 1051 MET cc_start: 0.8968 (mmm) cc_final: 0.8673 (mmm) REVERT: A 1152 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8318 (p) outliers start: 38 outliers final: 26 residues processed: 201 average time/residue: 0.1873 time to fit residues: 52.9650 Evaluate side-chains 203 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 101 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 48 optimal weight: 0.0040 chunk 73 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.141305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108661 restraints weight = 13785.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112855 restraints weight = 6055.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115551 restraints weight = 3553.814| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8780 Z= 0.118 Angle : 0.621 8.977 11851 Z= 0.321 Chirality : 0.041 0.221 1273 Planarity : 0.004 0.044 1521 Dihedral : 6.654 58.512 1164 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.02 % Favored : 91.59 % Rotamer: Outliers : 3.68 % Allowed : 24.53 % Favored : 71.79 % 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: -0.41 (0.27), residues: 1035 helix: 1.75 (0.30), residues: 307 sheet: -0.58 (0.37), residues: 218 loop : -1.43 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 258 HIS 0.004 0.001 HIS A 392 PHE 0.020 0.001 PHE A 900 TYR 0.028 0.001 TYR A 371 ARG 0.007 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 298) hydrogen bonds : angle 4.56684 ( 816) SS BOND : bond 0.00085 ( 1) SS BOND : angle 1.13990 ( 2) covalent geometry : bond 0.00264 ( 8779) covalent geometry : angle 0.62127 (11849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7162 (tmm-80) REVERT: A 64 PHE cc_start: 0.7659 (p90) cc_final: 0.7388 (p90) REVERT: A 69 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 127 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7852 (ttmt) REVERT: A 135 ASN cc_start: 0.8439 (t0) cc_final: 0.7527 (p0) REVERT: A 154 ASP cc_start: 0.7291 (t0) cc_final: 0.6997 (t0) REVERT: A 160 SER cc_start: 0.8177 (m) cc_final: 0.7827 (p) REVERT: A 190 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 210 MET cc_start: 0.8179 (mmm) cc_final: 0.7417 (mmm) REVERT: A 320 HIS cc_start: 0.7996 (m90) cc_final: 0.7322 (m-70) REVERT: A 354 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5573 (mmt180) REVERT: A 359 ASP cc_start: 0.5747 (m-30) cc_final: 0.5453 (m-30) REVERT: A 417 MET cc_start: 0.7869 (ttm) cc_final: 0.7637 (ttm) REVERT: A 419 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8267 (ttpt) REVERT: A 477 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7534 (tp-100) REVERT: A 487 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 548 GLN cc_start: 0.9123 (pt0) cc_final: 0.8661 (pm20) REVERT: A 651 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8077 (tp) REVERT: A 658 ASP cc_start: 0.8924 (m-30) cc_final: 0.8440 (m-30) REVERT: A 700 ARG cc_start: 0.9123 (ttp80) cc_final: 0.8863 (ttp80) REVERT: A 843 ASN cc_start: 0.8236 (m110) cc_final: 0.7793 (m110) REVERT: A 886 VAL cc_start: 0.7866 (t) cc_final: 0.7532 (m) REVERT: A 978 ASN cc_start: 0.8044 (m-40) cc_final: 0.7555 (t0) REVERT: A 996 ASN cc_start: 0.8389 (m-40) cc_final: 0.8000 (m-40) REVERT: A 997 TYR cc_start: 0.8001 (p90) cc_final: 0.7484 (p90) REVERT: A 1045 THR cc_start: 0.8083 (p) cc_final: 0.7796 (p) REVERT: A 1051 MET cc_start: 0.8956 (mmm) cc_final: 0.8666 (mmm) outliers start: 35 outliers final: 21 residues processed: 203 average time/residue: 0.1896 time to fit residues: 54.2415 Evaluate side-chains 191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1090 CYS Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 8.9990 chunk 79 optimal weight: 0.0970 chunk 96 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.0040 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 843 ASN A1025 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108100 restraints weight = 13825.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.112314 restraints weight = 6138.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115000 restraints weight = 3624.790| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8780 Z= 0.122 Angle : 0.635 9.569 11851 Z= 0.326 Chirality : 0.041 0.212 1273 Planarity : 0.004 0.044 1521 Dihedral : 6.220 53.954 1161 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.92 % Favored : 91.69 % Rotamer: Outliers : 2.74 % Allowed : 26.11 % Favored : 71.16 % 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: -0.41 (0.27), residues: 1035 helix: 1.77 (0.30), residues: 308 sheet: -0.65 (0.36), residues: 219 loop : -1.42 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 122 HIS 0.003 0.001 HIS A 327 PHE 0.027 0.002 PHE A 897 TYR 0.027 0.001 TYR A 371 ARG 0.006 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 298) hydrogen bonds : angle 4.52903 ( 816) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.03242 ( 2) covalent geometry : bond 0.00278 ( 8779) covalent geometry : angle 0.63489 (11849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7593 (tp40) cc_final: 0.7254 (tm-30) REVERT: A 20 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7181 (tmm-80) REVERT: A 64 PHE cc_start: 0.7671 (p90) cc_final: 0.7411 (p90) REVERT: A 69 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 127 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7850 (ttmt) REVERT: A 144 SER cc_start: 0.8642 (p) cc_final: 0.8311 (t) REVERT: A 154 ASP cc_start: 0.7278 (t0) cc_final: 0.6985 (t0) REVERT: A 160 SER cc_start: 0.8129 (m) cc_final: 0.7816 (p) REVERT: A 210 MET cc_start: 0.8039 (mmm) cc_final: 0.7488 (mmm) REVERT: A 320 HIS cc_start: 0.7869 (m90) cc_final: 0.7213 (m-70) REVERT: A 359 ASP cc_start: 0.5852 (m-30) cc_final: 0.5500 (m-30) REVERT: A 417 MET cc_start: 0.7873 (ttm) cc_final: 0.7618 (ttm) REVERT: A 419 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8223 (ttpt) REVERT: A 477 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7651 (tp-100) REVERT: A 487 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8241 (mt) REVERT: A 548 GLN cc_start: 0.9131 (pt0) cc_final: 0.8676 (pm20) REVERT: A 651 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8057 (tp) REVERT: A 658 ASP cc_start: 0.8950 (m-30) cc_final: 0.8466 (m-30) REVERT: A 700 ARG cc_start: 0.9113 (ttp80) cc_final: 0.8860 (ttp80) REVERT: A 843 ASN cc_start: 0.8221 (m-40) cc_final: 0.7738 (m-40) REVERT: A 886 VAL cc_start: 0.7840 (t) cc_final: 0.7497 (m) REVERT: A 897 PHE cc_start: 0.8704 (t80) cc_final: 0.8324 (t80) REVERT: A 901 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8481 (mm-40) REVERT: A 978 ASN cc_start: 0.8080 (m-40) cc_final: 0.7647 (t0) REVERT: A 997 TYR cc_start: 0.7987 (p90) cc_final: 0.7466 (p90) REVERT: A 1039 GLN cc_start: 0.8360 (mt0) cc_final: 0.7980 (mt0) REVERT: A 1045 THR cc_start: 0.8023 (p) cc_final: 0.7737 (p) REVERT: A 1051 MET cc_start: 0.8947 (mmm) cc_final: 0.8583 (mmt) REVERT: A 1186 MET cc_start: 0.8338 (mmm) cc_final: 0.7847 (mtp) outliers start: 26 outliers final: 17 residues processed: 194 average time/residue: 0.1805 time to fit residues: 50.1680 Evaluate side-chains 187 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1090 CYS Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 102 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 ASN A1024 ASN A1025 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.142307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109366 restraints weight = 13865.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.113652 restraints weight = 6117.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116337 restraints weight = 3599.307| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8780 Z= 0.120 Angle : 0.622 9.403 11851 Z= 0.319 Chirality : 0.042 0.197 1273 Planarity : 0.004 0.044 1521 Dihedral : 6.020 54.173 1159 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.83 % Favored : 91.69 % Rotamer: Outliers : 2.63 % Allowed : 26.11 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.27), residues: 1035 helix: 1.81 (0.30), residues: 308 sheet: -0.60 (0.37), residues: 216 loop : -1.40 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.003 0.001 HIS A 408 PHE 0.030 0.001 PHE A 897 TYR 0.027 0.001 TYR A 371 ARG 0.007 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 298) hydrogen bonds : angle 4.44922 ( 816) SS BOND : bond 0.00192 ( 1) SS BOND : angle 1.17566 ( 2) covalent geometry : bond 0.00274 ( 8779) covalent geometry : angle 0.62162 (11849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3741.73 seconds wall clock time: 65 minutes 54.33 seconds (3954.33 seconds total)