Starting phenix.real_space_refine on Thu Feb 13 05:25:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyx_37940/02_2025/8wyx_37940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyx_37940/02_2025/8wyx_37940.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/8wyx_37940/02_2025/8wyx_37940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyx_37940/02_2025/8wyx_37940.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyx_37940/02_2025/8wyx_37940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyx_37940/02_2025/8wyx_37940.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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 28 5.16 5 C 5663 2.51 5 N 1440 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8809 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8808 Classifications: {'peptide': 1070} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 1043} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.55 Number of scatterers: 8809 At special positions: 0 Unit cell: (96.264, 92.826, 91.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 28 16.00 O 1677 8.00 N 1440 7.00 C 5663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.09 Conformation dependent library (CDL) restraints added in 971.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 129 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 133 " 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 57.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.295A pdb=" N GLU A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.736A pdb=" N LEU A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.869A pdb=" N PHE A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.025A pdb=" N THR A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 324 through 325 No H-bonds generated for 'chain 'A' and resid 324 through 325' Processing helix chain 'A' and resid 326 through 330 removed outlier: 4.036A pdb=" N LYS A 329 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.813A pdb=" N TYR A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 439 removed outlier: 3.848A pdb=" N GLY A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 497 removed outlier: 3.501A pdb=" N GLU A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 517 Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.045A pdb=" N TYR A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 587 through 609 removed outlier: 3.902A pdb=" N ALA A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 629 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 663 through 667 removed outlier: 3.529A pdb=" N ASN A 667 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 679 removed outlier: 3.923A pdb=" N THR A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 696 Processing helix chain 'A' and resid 752 through 758 Processing helix chain 'A' and resid 758 through 768 removed outlier: 4.178A pdb=" N LEU A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 768 " --> pdb=" O THR A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 Processing helix chain 'A' and resid 825 through 838 Processing helix chain 'A' and resid 844 through 875 removed outlier: 3.584A pdb=" N GLY A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N TYR A 868 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 873 " --> pdb=" O ALA A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 891 through 908 Processing helix chain 'A' and resid 908 through 924 removed outlier: 4.132A pdb=" N LEU A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 936 through 947 removed outlier: 3.557A pdb=" N LEU A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 941 " --> pdb=" O TYR A 937 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 962 Processing helix chain 'A' and resid 979 through 988 Processing helix chain 'A' and resid 1024 through 1037 removed outlier: 3.827A pdb=" N VAL A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1071 through 1080 Processing helix chain 'A' and resid 1080 through 1092 Processing helix chain 'A' and resid 1093 through 1109 Processing helix chain 'A' and resid 1114 through 1128 Processing helix chain 'A' and resid 1130 through 1143 Processing helix chain 'A' and resid 1145 through 1159 Processing helix chain 'A' and resid 1160 through 1164 Processing helix chain 'A' and resid 1173 through 1183 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 79 removed outlier: 5.619A pdb=" N ILE A 73 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN A 90 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 75 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 97 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 307 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 103 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THR A 164 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 170 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA A 162 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET A 172 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 160 " --> pdb=" O MET A 172 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 174 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 354 removed outlier: 6.060A pdb=" N PHE A 348 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU A 583 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 350 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU A 585 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS A 352 " --> pdb=" O GLU A 585 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN A 363 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 464 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 457 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 449 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER A 459 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 447 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 658 through 662 Processing sheet with id=AA5, first strand: chain 'A' and resid 1050 through 1055 removed outlier: 3.623A pdb=" N VAL A1009 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN A1166 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 997 " --> pdb=" O LYS A1188 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL A1190 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 999 " --> pdb=" O VAL A1190 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1446 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: 3.08 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2810 1.34 - 1.45: 1198 1.45 - 1.57: 4922 1.57 - 1.69: 1 1.69 - 1.80: 54 Bond restraints: 8985 Sorted by residual: bond pdb=" CB ASN A 267 " pdb=" CG ASN A 267 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" CG PRO A 347 " pdb=" CD PRO A 347 " ideal model delta sigma weight residual 1.512 1.479 0.033 2.70e-02 1.37e+03 1.51e+00 bond pdb=" CG GLU A 622 " pdb=" CD GLU A 622 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.40e+00 bond pdb=" SD MET A 263 " pdb=" CE MET A 263 " ideal model delta sigma weight residual 1.791 1.762 0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CA ASN A 669 " pdb=" CB ASN A 669 " ideal model delta sigma weight residual 1.539 1.593 -0.054 4.88e-02 4.20e+02 1.21e+00 ... (remaining 8980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11798 1.53 - 3.05: 264 3.05 - 4.58: 32 4.58 - 6.11: 4 6.11 - 7.64: 2 Bond angle restraints: 12100 Sorted by residual: angle pdb=" N GLU A 622 " pdb=" CA GLU A 622 " pdb=" CB GLU A 622 " ideal model delta sigma weight residual 110.16 114.31 -4.15 1.48e+00 4.57e-01 7.88e+00 angle pdb=" C PHE A 621 " pdb=" N GLU A 622 " pdb=" CA GLU A 622 " ideal model delta sigma weight residual 120.29 116.87 3.42 1.42e+00 4.96e-01 5.79e+00 angle pdb=" N GLY A 154 " pdb=" CA GLY A 154 " pdb=" C GLY A 154 " ideal model delta sigma weight residual 113.18 118.51 -5.33 2.37e+00 1.78e-01 5.06e+00 angle pdb=" CA LEU A1002 " pdb=" CB LEU A1002 " pdb=" CG LEU A1002 " ideal model delta sigma weight residual 116.30 123.94 -7.64 3.50e+00 8.16e-02 4.76e+00 angle pdb=" N GLY A1114 " pdb=" CA GLY A1114 " pdb=" C GLY A1114 " ideal model delta sigma weight residual 110.77 114.93 -4.16 1.93e+00 2.68e-01 4.64e+00 ... (remaining 12095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 4841 16.61 - 33.21: 517 33.21 - 49.82: 89 49.82 - 66.42: 8 66.42 - 83.03: 6 Dihedral angle restraints: 5461 sinusoidal: 2278 harmonic: 3183 Sorted by residual: dihedral pdb=" CA HIS A 750 " pdb=" C HIS A 750 " pdb=" N LEU A 751 " pdb=" CA LEU A 751 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A 424 " pdb=" C ILE A 424 " pdb=" N HIS A 425 " pdb=" CA HIS A 425 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU A1002 " pdb=" C LEU A1002 " pdb=" N PRO A1003 " pdb=" CA PRO A1003 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 748 0.032 - 0.064: 398 0.064 - 0.096: 118 0.096 - 0.128: 51 0.128 - 0.159: 8 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA GLU A 622 " pdb=" N GLU A 622 " pdb=" C GLU A 622 " pdb=" CB GLU A 622 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA THR A 737 " pdb=" N THR A 737 " pdb=" C THR A 737 " pdb=" CB THR A 737 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE A 445 " pdb=" N ILE A 445 " pdb=" C ILE A 445 " pdb=" CB ILE A 445 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1320 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1068 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A1069 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1069 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1069 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 297 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 298 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 488 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C ASN A 488 " 0.023 2.00e-02 2.50e+03 pdb=" O ASN A 488 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A 489 " -0.008 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 89 2.60 - 3.18: 7753 3.18 - 3.75: 13794 3.75 - 4.33: 19973 4.33 - 4.90: 32676 Nonbonded interactions: 74285 Sorted by model distance: nonbonded pdb=" OE1 GLU A 243 " pdb="ZN ZN A1201 " model vdw 2.029 2.230 nonbonded pdb=" O LEU A 151 " pdb=" OG1 THR A 155 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR A 413 " pdb=" OD2 ASP A 451 " model vdw 2.106 3.040 nonbonded pdb=" OG SER A 139 " pdb=" OD2 ASP A 190 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR A 241 " pdb=" OE2 GLU A 598 " model vdw 2.206 3.040 ... (remaining 74280 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: 0.120 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 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 : 0.005 0.054 8985 Z= 0.343 Angle : 0.568 7.636 12100 Z= 0.322 Chirality : 0.044 0.159 1323 Planarity : 0.004 0.043 1544 Dihedral : 13.609 83.031 3405 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.20 % Allowed : 0.30 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.06 (0.25), residues: 1062 helix: 0.90 (0.22), residues: 528 sheet: -0.77 (0.35), residues: 197 loop : -0.93 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.006 0.001 HIS A 578 PHE 0.018 0.002 PHE A 621 TYR 0.020 0.002 TYR A 660 ARG 0.004 0.001 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.7411 (tt0) cc_final: 0.6875 (tp30) REVERT: A 446 ASP cc_start: 0.8058 (p0) cc_final: 0.7647 (p0) REVERT: A 695 TYR cc_start: 0.5042 (m-80) cc_final: 0.4148 (m-80) REVERT: A 784 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8258 (mt-10) REVERT: A 790 MET cc_start: 0.6218 (ttt) cc_final: 0.5755 (ttt) REVERT: A 991 ASP cc_start: 0.4559 (m-30) cc_final: 0.3841 (t0) REVERT: A 1012 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7651 (p) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.2424 time to fit residues: 82.0853 Evaluate side-chains 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1012 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 97 GLN A 166 ASN A 177 ASN A 295 ASN A 425 HIS A 572 HIS ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN A 750 HIS ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.115350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.095236 restraints weight = 22813.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.098220 restraints weight = 11714.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.100217 restraints weight = 7559.870| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8985 Z= 0.373 Angle : 0.740 13.359 12100 Z= 0.390 Chirality : 0.047 0.232 1323 Planarity : 0.005 0.060 1544 Dihedral : 5.244 57.511 1152 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.63 % Allowed : 11.35 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.14 (0.25), residues: 1062 helix: 0.75 (0.21), residues: 540 sheet: -0.83 (0.37), residues: 196 loop : -0.83 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A1039 HIS 0.006 0.002 HIS A 157 PHE 0.025 0.003 PHE A 165 TYR 0.020 0.003 TYR A1150 ARG 0.009 0.001 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 THR cc_start: 0.8540 (m) cc_final: 0.8276 (p) REVERT: A 309 ASN cc_start: 0.8051 (m-40) cc_final: 0.7573 (m110) REVERT: A 501 SER cc_start: 0.8663 (m) cc_final: 0.8383 (p) REVERT: A 872 MET cc_start: 0.8421 (tmm) cc_final: 0.7927 (tmm) REVERT: A 920 ARG cc_start: 0.8586 (tmm-80) cc_final: 0.8235 (ttp-110) REVERT: A 991 ASP cc_start: 0.6164 (m-30) cc_final: 0.5184 (t0) REVERT: A 1011 MET cc_start: 0.6846 (ttm) cc_final: 0.6454 (ttt) outliers start: 26 outliers final: 16 residues processed: 174 average time/residue: 0.2133 time to fit residues: 51.7645 Evaluate side-chains 143 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 750 HIS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1043 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 578 HIS ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.116711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.096573 restraints weight = 22826.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.099659 restraints weight = 11661.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.101680 restraints weight = 7501.345| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8985 Z= 0.233 Angle : 0.611 7.898 12100 Z= 0.323 Chirality : 0.044 0.174 1323 Planarity : 0.004 0.046 1544 Dihedral : 4.654 14.746 1151 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.03 % Allowed : 14.99 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.16 (0.26), residues: 1062 helix: 1.07 (0.21), residues: 539 sheet: -0.84 (0.37), residues: 196 loop : -0.72 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1039 HIS 0.016 0.001 HIS A 750 PHE 0.020 0.002 PHE A 691 TYR 0.039 0.002 TYR A1150 ARG 0.005 0.001 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASN cc_start: 0.8128 (m-40) cc_final: 0.7686 (m110) REVERT: A 369 TRP cc_start: 0.6999 (m-90) cc_final: 0.6306 (m-90) REVERT: A 432 TYR cc_start: 0.7807 (t80) cc_final: 0.7559 (t80) REVERT: A 487 MET cc_start: 0.8465 (mmm) cc_final: 0.8108 (mmm) REVERT: A 501 SER cc_start: 0.8597 (m) cc_final: 0.8314 (p) REVERT: A 636 HIS cc_start: 0.8108 (t-170) cc_final: 0.7837 (t-170) REVERT: A 683 MET cc_start: 0.8067 (tpp) cc_final: 0.7837 (tpp) REVERT: A 691 PHE cc_start: 0.8789 (t80) cc_final: 0.8295 (t80) REVERT: A 872 MET cc_start: 0.8359 (tmm) cc_final: 0.7835 (tmm) REVERT: A 1029 ILE cc_start: 0.8488 (mt) cc_final: 0.8264 (mp) REVERT: A 1063 PHE cc_start: 0.8370 (m-80) cc_final: 0.8122 (m-80) outliers start: 20 outliers final: 10 residues processed: 154 average time/residue: 0.2182 time to fit residues: 47.1686 Evaluate side-chains 132 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1071 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 106 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN A1103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.112757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.093063 restraints weight = 23102.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.096062 restraints weight = 11918.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.098030 restraints weight = 7682.770| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8985 Z= 0.304 Angle : 0.665 14.982 12100 Z= 0.348 Chirality : 0.045 0.172 1323 Planarity : 0.004 0.044 1544 Dihedral : 4.749 16.127 1151 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.24 % Allowed : 16.31 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.10 (0.26), residues: 1062 helix: 0.85 (0.21), residues: 540 sheet: -0.96 (0.37), residues: 194 loop : -0.87 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1039 HIS 0.005 0.001 HIS A 157 PHE 0.017 0.002 PHE A 165 TYR 0.030 0.002 TYR A1150 ARG 0.004 0.001 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.6546 (ttm) cc_final: 0.6337 (ttm) REVERT: A 230 LYS cc_start: 0.6939 (mttt) cc_final: 0.6443 (pttt) REVERT: A 372 ASN cc_start: 0.7411 (p0) cc_final: 0.7107 (p0) REVERT: A 501 SER cc_start: 0.8713 (m) cc_final: 0.8379 (p) REVERT: A 616 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8804 (tm-30) REVERT: A 636 HIS cc_start: 0.8350 (t-170) cc_final: 0.8134 (t-170) REVERT: A 674 TYR cc_start: 0.4041 (OUTLIER) cc_final: 0.3301 (t80) REVERT: A 684 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7913 (mp) REVERT: A 872 MET cc_start: 0.8436 (tmm) cc_final: 0.7856 (tmm) REVERT: A 920 ARG cc_start: 0.8832 (ptt-90) cc_final: 0.8463 (ptt90) REVERT: A 961 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7390 (t0) REVERT: A 1006 VAL cc_start: 0.4854 (OUTLIER) cc_final: 0.4593 (m) REVERT: A 1011 MET cc_start: 0.6656 (ttm) cc_final: 0.6409 (ttt) REVERT: A 1029 ILE cc_start: 0.8521 (mt) cc_final: 0.8241 (mp) REVERT: A 1067 ARG cc_start: 0.7966 (mmp80) cc_final: 0.7599 (mmp80) REVERT: A 1113 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.5141 (ptt-90) outliers start: 32 outliers final: 17 residues processed: 158 average time/residue: 0.2344 time to fit residues: 50.5720 Evaluate side-chains 141 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1113 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 194 GLN ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.110666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.091643 restraints weight = 23119.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.094501 restraints weight = 12051.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.096405 restraints weight = 7805.761| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8985 Z= 0.300 Angle : 0.653 13.857 12100 Z= 0.343 Chirality : 0.044 0.153 1323 Planarity : 0.004 0.042 1544 Dihedral : 4.816 19.241 1151 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.95 % Allowed : 17.43 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.26), residues: 1062 helix: 0.79 (0.21), residues: 540 sheet: -1.07 (0.37), residues: 190 loop : -0.97 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A1039 HIS 0.010 0.001 HIS A 878 PHE 0.016 0.002 PHE A1187 TYR 0.027 0.002 TYR A1150 ARG 0.008 0.001 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.6798 (mttt) cc_final: 0.6395 (pttt) REVERT: A 372 ASN cc_start: 0.7533 (p0) cc_final: 0.7320 (p0) REVERT: A 487 MET cc_start: 0.8446 (mmm) cc_final: 0.8186 (mmm) REVERT: A 501 SER cc_start: 0.8701 (m) cc_final: 0.8356 (p) REVERT: A 520 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5806 (tttp) REVERT: A 563 MET cc_start: 0.8809 (mmm) cc_final: 0.8564 (mmm) REVERT: A 616 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8863 (tm-30) REVERT: A 617 VAL cc_start: 0.9455 (t) cc_final: 0.9118 (t) REVERT: A 691 PHE cc_start: 0.8767 (t80) cc_final: 0.8320 (t80) REVERT: A 872 MET cc_start: 0.8362 (tmm) cc_final: 0.7950 (ppp) REVERT: A 920 ARG cc_start: 0.8852 (ptt-90) cc_final: 0.8418 (ptt90) REVERT: A 936 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7274 (t70) REVERT: A 1029 ILE cc_start: 0.8487 (mt) cc_final: 0.8182 (mp) REVERT: A 1067 ARG cc_start: 0.7901 (mmp80) cc_final: 0.7658 (mmp80) outliers start: 39 outliers final: 26 residues processed: 162 average time/residue: 0.2180 time to fit residues: 49.2069 Evaluate side-chains 147 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1103 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.108319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.089644 restraints weight = 23445.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.092357 restraints weight = 12362.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.094196 restraints weight = 8113.882| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8985 Z= 0.364 Angle : 0.717 14.505 12100 Z= 0.378 Chirality : 0.046 0.164 1323 Planarity : 0.004 0.045 1544 Dihedral : 5.046 17.688 1151 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.56 % Allowed : 18.03 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.62 (0.25), residues: 1062 helix: 0.51 (0.21), residues: 539 sheet: -1.18 (0.37), residues: 183 loop : -1.28 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1039 HIS 0.009 0.002 HIS A 878 PHE 0.016 0.002 PHE A 165 TYR 0.026 0.003 TYR A 564 ARG 0.004 0.001 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7049 (mttt) cc_final: 0.6666 (pttt) REVERT: A 501 SER cc_start: 0.8739 (m) cc_final: 0.8357 (p) REVERT: A 563 MET cc_start: 0.8633 (mmm) cc_final: 0.8342 (mmm) REVERT: A 616 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8944 (tm-30) REVERT: A 617 VAL cc_start: 0.9474 (t) cc_final: 0.9143 (t) REVERT: A 694 LYS cc_start: 0.8369 (ptpp) cc_final: 0.8133 (tptt) REVERT: A 750 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.5574 (p90) REVERT: A 872 MET cc_start: 0.8438 (tmm) cc_final: 0.8049 (ppp) REVERT: A 920 ARG cc_start: 0.8861 (ptt-90) cc_final: 0.8372 (ptt90) REVERT: A 978 MET cc_start: 0.5020 (ppp) cc_final: 0.4584 (ppp) REVERT: A 1007 ASN cc_start: 0.7853 (m-40) cc_final: 0.7599 (t0) REVERT: A 1029 ILE cc_start: 0.8466 (mt) cc_final: 0.8179 (mp) outliers start: 45 outliers final: 34 residues processed: 166 average time/residue: 0.2201 time to fit residues: 50.8216 Evaluate side-chains 160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 750 HIS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1103 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 HIS ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.108113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.088558 restraints weight = 24247.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.091342 restraints weight = 12976.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.093256 restraints weight = 8580.516| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8985 Z= 0.324 Angle : 0.694 13.066 12100 Z= 0.363 Chirality : 0.045 0.177 1323 Planarity : 0.004 0.045 1544 Dihedral : 5.009 19.202 1151 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.86 % Allowed : 18.54 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.64 (0.25), residues: 1062 helix: 0.55 (0.21), residues: 539 sheet: -1.24 (0.36), residues: 187 loop : -1.37 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1039 HIS 0.008 0.002 HIS A 878 PHE 0.022 0.002 PHE A 691 TYR 0.034 0.002 TYR A1150 ARG 0.004 0.001 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7101 (mttt) cc_final: 0.6788 (pttt) REVERT: A 372 ASN cc_start: 0.7538 (p0) cc_final: 0.7337 (p0) REVERT: A 501 SER cc_start: 0.8661 (m) cc_final: 0.8273 (p) REVERT: A 563 MET cc_start: 0.8539 (mmm) cc_final: 0.8243 (mmm) REVERT: A 616 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8901 (tm-30) REVERT: A 617 VAL cc_start: 0.9482 (t) cc_final: 0.9142 (t) REVERT: A 750 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.5641 (p90) REVERT: A 872 MET cc_start: 0.8463 (tmm) cc_final: 0.8088 (ppp) REVERT: A 920 ARG cc_start: 0.8871 (ptt-90) cc_final: 0.8393 (ptt90) REVERT: A 978 MET cc_start: 0.4707 (ppp) cc_final: 0.4239 (ppp) REVERT: A 1007 ASN cc_start: 0.7757 (m-40) cc_final: 0.7481 (m-40) REVERT: A 1012 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8207 (t) REVERT: A 1029 ILE cc_start: 0.8449 (mt) cc_final: 0.8177 (mp) outliers start: 48 outliers final: 33 residues processed: 165 average time/residue: 0.2145 time to fit residues: 49.6820 Evaluate side-chains 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 750 HIS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1103 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 658 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.109540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.090176 restraints weight = 24239.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.092978 restraints weight = 12736.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.094840 restraints weight = 8312.079| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8985 Z= 0.279 Angle : 0.675 9.750 12100 Z= 0.353 Chirality : 0.046 0.329 1323 Planarity : 0.004 0.044 1544 Dihedral : 4.883 16.795 1151 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.44 % Allowed : 19.76 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.25), residues: 1062 helix: 0.67 (0.21), residues: 540 sheet: -1.20 (0.37), residues: 183 loop : -1.34 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1039 HIS 0.005 0.001 HIS A 636 PHE 0.025 0.002 PHE A 691 TYR 0.035 0.002 TYR A1150 ARG 0.004 0.001 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7851 (ttm) cc_final: 0.7608 (tpp) REVERT: A 487 MET cc_start: 0.8191 (mmm) cc_final: 0.7899 (mmm) REVERT: A 501 SER cc_start: 0.8611 (m) cc_final: 0.8217 (p) REVERT: A 563 MET cc_start: 0.8560 (mmm) cc_final: 0.8147 (mmm) REVERT: A 616 GLN cc_start: 0.9184 (tm-30) cc_final: 0.8927 (tm-30) REVERT: A 617 VAL cc_start: 0.9466 (t) cc_final: 0.9133 (t) REVERT: A 750 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.5714 (p90) REVERT: A 872 MET cc_start: 0.8436 (tmm) cc_final: 0.8072 (ppp) REVERT: A 920 ARG cc_start: 0.8851 (ptt-90) cc_final: 0.8394 (ptt90) REVERT: A 978 MET cc_start: 0.4938 (ppp) cc_final: 0.4438 (ppp) REVERT: A 1029 ILE cc_start: 0.8498 (mt) cc_final: 0.8227 (mp) outliers start: 34 outliers final: 29 residues processed: 154 average time/residue: 0.2230 time to fit residues: 48.2504 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 750 HIS Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1103 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 overall best weight: 3.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.109084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.089754 restraints weight = 24855.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.092587 restraints weight = 12919.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.094479 restraints weight = 8410.441| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 8985 Z= 0.262 Angle : 0.671 10.460 12100 Z= 0.350 Chirality : 0.044 0.259 1323 Planarity : 0.004 0.041 1544 Dihedral : 4.784 20.813 1151 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.95 % Allowed : 20.06 % Favored : 75.99 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.85 % 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: -0.46 (0.25), residues: 1062 helix: 0.78 (0.21), residues: 540 sheet: -1.24 (0.36), residues: 187 loop : -1.38 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1039 HIS 0.004 0.001 HIS A 820 PHE 0.030 0.002 PHE A 691 TYR 0.035 0.002 TYR A1150 ARG 0.003 0.000 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7897 (ttm) cc_final: 0.7619 (ttm) REVERT: A 487 MET cc_start: 0.8219 (mmm) cc_final: 0.7868 (mmm) REVERT: A 501 SER cc_start: 0.8566 (m) cc_final: 0.8162 (p) REVERT: A 563 MET cc_start: 0.8546 (mmm) cc_final: 0.8132 (mmm) REVERT: A 628 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7551 (ptpt) REVERT: A 688 MET cc_start: 0.8775 (mmm) cc_final: 0.8569 (mpp) REVERT: A 768 GLU cc_start: 0.6766 (tp30) cc_final: 0.6170 (mm-30) REVERT: A 872 MET cc_start: 0.8440 (tmm) cc_final: 0.8075 (ppp) REVERT: A 920 ARG cc_start: 0.8851 (ptt-90) cc_final: 0.8383 (ptt90) REVERT: A 978 MET cc_start: 0.4789 (ppp) cc_final: 0.4067 (ppp) REVERT: A 982 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7209 (mp0) REVERT: A 1029 ILE cc_start: 0.8524 (mt) cc_final: 0.8246 (mp) outliers start: 39 outliers final: 33 residues processed: 158 average time/residue: 0.2237 time to fit residues: 48.8621 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1103 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 658 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.108487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.089367 restraints weight = 24791.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.092203 restraints weight = 12871.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.094064 restraints weight = 8362.522| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 8985 Z= 0.282 Angle : 0.714 13.365 12100 Z= 0.370 Chirality : 0.045 0.253 1323 Planarity : 0.004 0.040 1544 Dihedral : 4.815 19.953 1151 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.05 % Allowed : 20.36 % Favored : 75.58 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.85 % 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: -0.60 (0.25), residues: 1062 helix: 0.63 (0.21), residues: 541 sheet: -1.23 (0.36), residues: 193 loop : -1.44 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1039 HIS 0.004 0.001 HIS A 750 PHE 0.026 0.002 PHE A 691 TYR 0.035 0.002 TYR A1150 ARG 0.003 0.001 ARG A1112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7906 (ttm) cc_final: 0.7640 (tpp) REVERT: A 487 MET cc_start: 0.8218 (mmm) cc_final: 0.7911 (mmm) REVERT: A 501 SER cc_start: 0.8606 (m) cc_final: 0.8212 (p) REVERT: A 563 MET cc_start: 0.8588 (mmm) cc_final: 0.8313 (mmm) REVERT: A 628 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7567 (ptpt) REVERT: A 750 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.5750 (p90) REVERT: A 790 MET cc_start: 0.6544 (tmm) cc_final: 0.5733 (tmm) REVERT: A 872 MET cc_start: 0.8554 (tmm) cc_final: 0.8054 (tmm) REVERT: A 920 ARG cc_start: 0.8844 (ptt-90) cc_final: 0.8360 (ptt90) REVERT: A 978 MET cc_start: 0.4741 (ppp) cc_final: 0.4011 (ppp) REVERT: A 1029 ILE cc_start: 0.8488 (mt) cc_final: 0.8214 (mp) outliers start: 40 outliers final: 35 residues processed: 160 average time/residue: 0.2119 time to fit residues: 47.2882 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 750 HIS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.0030 chunk 80 optimal weight: 6.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.108807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.089905 restraints weight = 24236.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.092770 restraints weight = 12308.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.094710 restraints weight = 7894.895| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.7081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 8985 Z= 0.263 Angle : 0.712 13.614 12100 Z= 0.367 Chirality : 0.045 0.251 1323 Planarity : 0.004 0.039 1544 Dihedral : 4.769 20.512 1151 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.15 % Allowed : 20.36 % Favored : 75.48 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.85 % 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: -0.55 (0.25), residues: 1062 helix: 0.66 (0.21), residues: 540 sheet: -1.19 (0.36), residues: 190 loop : -1.42 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1039 HIS 0.004 0.001 HIS A 750 PHE 0.029 0.002 PHE A 691 TYR 0.035 0.002 TYR A1150 ARG 0.003 0.000 ARG A1112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.21 seconds wall clock time: 49 minutes 58.06 seconds (2998.06 seconds total)