Starting phenix.real_space_refine on Wed Feb 12 12:11:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h4u_34484/02_2025/8h4u_34484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h4u_34484/02_2025/8h4u_34484.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/8h4u_34484/02_2025/8h4u_34484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h4u_34484/02_2025/8h4u_34484.map" model { file = "/net/cci-nas-00/data/ceres_data/8h4u_34484/02_2025/8h4u_34484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h4u_34484/02_2025/8h4u_34484.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= 0.003 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 34 5.16 5 C 5041 2.51 5 N 1418 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7944 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7944 Classifications: {'peptide': 959} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 932} Chain breaks: 4 Time building chain proxies: 4.69, per 1000 atoms: 0.59 Number of scatterers: 7944 At special positions: 0 Unit cell: (96.05, 90.95, 110.5, 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 34 16.00 O 1451 8.00 N 1418 7.00 C 5041 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: 2.20 Conformation dependent library (CDL) restraints added in 918.0 milliseconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 73.1% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.749A pdb=" N LEU A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 272 Processing helix chain 'A' and resid 275 through 294 removed outlier: 3.789A pdb=" N TYR A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 321 through 352 removed outlier: 3.655A pdb=" N VAL A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 394 removed outlier: 3.558A pdb=" N SER A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.630A pdb=" N ASP A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.846A pdb=" N ASP A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 496 Processing helix chain 'A' and resid 505 through 517 Processing helix chain 'A' and resid 522 through 535 Processing helix chain 'A' and resid 535 through 547 removed outlier: 3.830A pdb=" N ALA A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.556A pdb=" N PHE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 674 removed outlier: 3.649A pdb=" N ILE A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 removed outlier: 3.699A pdb=" N GLU A 678 " --> pdb=" O HIS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 689 through 703 removed outlier: 3.597A pdb=" N VAL A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 6.257A pdb=" N ASN A 707 " --> pdb=" O GLN A 704 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 709 " --> pdb=" O PRO A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 726 through 743 removed outlier: 3.592A pdb=" N ARG A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 776 removed outlier: 3.675A pdb=" N GLN A 750 " --> pdb=" O ARG A 746 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 756 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 removed outlier: 3.722A pdb=" N MET A 784 " --> pdb=" O TYR A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.884A pdb=" N ALA A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 827 removed outlier: 3.608A pdb=" N VAL A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 829 through 850 Processing helix chain 'A' and resid 858 through 876 Processing helix chain 'A' and resid 884 through 889 Processing helix chain 'A' and resid 891 through 899 removed outlier: 3.746A pdb=" N ALA A 894 " --> pdb=" O ALA A 891 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 895 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU A 896 " --> pdb=" O GLU A 893 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASP A 897 " --> pdb=" O ALA A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 921 through 931 removed outlier: 3.697A pdb=" N LEU A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 940 removed outlier: 3.934A pdb=" N LYS A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 956 Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 999 through 1019 removed outlier: 3.714A pdb=" N LYS A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A1004 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1057 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1065 through 1074 removed outlier: 3.962A pdb=" N VAL A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A1070 " --> pdb=" O GLU A1066 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A1073 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1086 Processing helix chain 'A' and resid 1088 through 1095 Processing helix chain 'A' and resid 1096 through 1098 No H-bonds generated for 'chain 'A' and resid 1096 through 1098' Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1116 removed outlier: 3.748A pdb=" N ASP A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1121 Processing helix chain 'A' and resid 1134 through 1147 Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1155 through 1168 removed outlier: 3.789A pdb=" N LYS A1159 " --> pdb=" O ASN A1155 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A1168 " --> pdb=" O ILE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1180 No H-bonds generated for 'chain 'A' and resid 1178 through 1180' Processing helix chain 'A' and resid 1209 through 1221 removed outlier: 3.536A pdb=" N ILE A1213 " --> pdb=" O GLY A1209 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1219 " --> pdb=" O THR A1215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'A' and resid 1170 through 1176 removed outlier: 4.144A pdb=" N ASP A1186 " --> pdb=" O ARG A1173 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR A1175 " --> pdb=" O ILE A1184 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE A1184 " --> pdb=" O THR A1175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1191 through 1194 447 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2651 1.34 - 1.46: 1776 1.46 - 1.58: 3609 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 8092 Sorted by residual: bond pdb=" N HIS A 500 " pdb=" CA HIS A 500 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.90e+00 bond pdb=" C TYR A1222 " pdb=" O TYR A1222 " ideal model delta sigma weight residual 1.244 1.229 0.015 9.10e-03 1.21e+04 2.59e+00 bond pdb=" CA ASP A1150 " pdb=" CB ASP A1150 " ideal model delta sigma weight residual 1.535 1.564 -0.029 1.90e-02 2.77e+03 2.37e+00 bond pdb=" C ASN A 405 " pdb=" N PRO A 406 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.48e+00 bond pdb=" CG GLU A 267 " pdb=" CD GLU A 267 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.22e+00 ... (remaining 8087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10716 2.10 - 4.20: 124 4.20 - 6.30: 18 6.30 - 8.40: 5 8.40 - 10.49: 4 Bond angle restraints: 10867 Sorted by residual: angle pdb=" N GLU A 267 " pdb=" CA GLU A 267 " pdb=" CB GLU A 267 " ideal model delta sigma weight residual 110.28 117.19 -6.91 1.55e+00 4.16e-01 1.99e+01 angle pdb=" C ARG A 266 " pdb=" N GLU A 267 " pdb=" CA GLU A 267 " ideal model delta sigma weight residual 120.31 113.54 6.77 1.52e+00 4.33e-01 1.98e+01 angle pdb=" CA TYR A1222 " pdb=" C TYR A1222 " pdb=" N PRO A1223 " ideal model delta sigma weight residual 120.58 117.78 2.80 7.40e-01 1.83e+00 1.43e+01 angle pdb=" C HIS A 500 " pdb=" CA HIS A 500 " pdb=" CB HIS A 500 " ideal model delta sigma weight residual 110.42 117.94 -7.52 1.99e+00 2.53e-01 1.43e+01 angle pdb=" CB MET A 903 " pdb=" CG MET A 903 " pdb=" SD MET A 903 " ideal model delta sigma weight residual 112.70 123.19 -10.49 3.00e+00 1.11e-01 1.22e+01 ... (remaining 10862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4122 17.91 - 35.83: 639 35.83 - 53.74: 166 53.74 - 71.66: 37 71.66 - 89.57: 11 Dihedral angle restraints: 4975 sinusoidal: 2156 harmonic: 2819 Sorted by residual: dihedral pdb=" CA HIS A 500 " pdb=" C HIS A 500 " pdb=" N TYR A 501 " pdb=" CA TYR A 501 " ideal model delta harmonic sigma weight residual 180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CB GLU A 896 " pdb=" CG GLU A 896 " pdb=" CD GLU A 896 " pdb=" OE1 GLU A 896 " ideal model delta sinusoidal sigma weight residual 0.00 89.57 -89.57 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 853 " pdb=" CG GLU A 853 " pdb=" CD GLU A 853 " pdb=" OE1 GLU A 853 " ideal model delta sinusoidal sigma weight residual 0.00 -88.82 88.82 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 4972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 806 0.030 - 0.060: 236 0.060 - 0.089: 79 0.089 - 0.119: 36 0.119 - 0.149: 3 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA GLU A 267 " pdb=" N GLU A 267 " pdb=" C GLU A 267 " pdb=" CB GLU A 267 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1157 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 267 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU A 267 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU A 267 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU A 267 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 618 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LYS A 618 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS A 618 " -0.010 2.00e-02 2.50e+03 pdb=" N TRP A 619 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 578 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C MET A 578 " 0.027 2.00e-02 2.50e+03 pdb=" O MET A 578 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 579 " -0.009 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1059 2.75 - 3.29: 7726 3.29 - 3.83: 12623 3.83 - 4.36: 14512 4.36 - 4.90: 24999 Nonbonded interactions: 60919 Sorted by model distance: nonbonded pdb=" O PHE A 414 " pdb=" ND2 ASN A 481 " model vdw 2.218 3.120 nonbonded pdb=" O LEU A 781 " pdb=" OG SER A 785 " model vdw 2.263 3.040 nonbonded pdb=" O ASP A 897 " pdb=" NZ LYS A 944 " model vdw 2.297 3.120 nonbonded pdb=" OD2 ASP A 532 " pdb=" NH2 ARG A 826 " model vdw 2.301 3.120 nonbonded pdb=" O ARG A1070 " pdb=" OG SER A1074 " model vdw 2.322 3.040 ... (remaining 60914 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: 0.550 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.090 Find NCS groups from input model: 0.070 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.002 0.050 8092 Z= 0.141 Angle : 0.593 10.494 10867 Z= 0.323 Chirality : 0.035 0.149 1160 Planarity : 0.003 0.036 1402 Dihedral : 18.356 89.569 3149 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.28 % Allowed : 24.83 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.27), residues: 949 helix: 0.89 (0.20), residues: 617 sheet: -1.17 (1.01), residues: 32 loop : -1.59 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 619 HIS 0.008 0.001 HIS A 500 PHE 0.012 0.001 PHE A 882 TYR 0.015 0.001 TYR A 282 ARG 0.002 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.896 Fit side-chains REVERT: A 325 MET cc_start: 0.7237 (ttp) cc_final: 0.6933 (ttp) REVERT: A 879 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7185 (tp30) REVERT: A 1196 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6138 (ptpt) outliers start: 11 outliers final: 2 residues processed: 100 average time/residue: 0.2005 time to fit residues: 28.1244 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 1196 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN A 535 ASN A 674 HIS A 697 ASN A 712 HIS A 775 HIS A 837 GLN A 905 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128092 restraints weight = 10916.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125300 restraints weight = 8916.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126438 restraints weight = 10903.086| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8092 Z= 0.277 Angle : 0.617 11.693 10867 Z= 0.323 Chirality : 0.041 0.154 1160 Planarity : 0.004 0.036 1402 Dihedral : 5.077 62.871 1083 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.03 % Allowed : 23.19 % Favored : 73.78 % 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: 0.75 (0.28), residues: 949 helix: 1.45 (0.21), residues: 646 sheet: -1.46 (0.93), residues: 33 loop : -1.60 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 959 HIS 0.007 0.002 HIS A 500 PHE 0.029 0.002 PHE A 283 TYR 0.014 0.002 TYR A 755 ARG 0.003 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.902 Fit side-chains REVERT: A 904 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8306 (pptt) REVERT: A 1006 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8011 (mmt180) REVERT: A 1043 ASP cc_start: 0.7615 (m-30) cc_final: 0.7257 (m-30) REVERT: A 1089 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: A 1196 LYS cc_start: 0.6359 (OUTLIER) cc_final: 0.5158 (pttt) outliers start: 26 outliers final: 11 residues processed: 118 average time/residue: 0.1964 time to fit residues: 32.0610 Evaluate side-chains 99 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1196 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 423 HIS A 503 ASN A 674 HIS A 915 ASN A1168 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130486 restraints weight = 11015.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128084 restraints weight = 9226.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128846 restraints weight = 10284.080| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8092 Z= 0.164 Angle : 0.553 14.816 10867 Z= 0.284 Chirality : 0.038 0.225 1160 Planarity : 0.003 0.035 1402 Dihedral : 4.001 54.261 1076 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.80 % Allowed : 23.08 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 949 helix: 1.85 (0.21), residues: 648 sheet: -1.05 (0.93), residues: 32 loop : -1.49 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 850 HIS 0.006 0.001 HIS A 500 PHE 0.018 0.001 PHE A 283 TYR 0.014 0.001 TYR A 755 ARG 0.004 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 516 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8195 (mtmt) REVERT: A 731 MET cc_start: 0.4065 (ttt) cc_final: 0.3783 (ttm) REVERT: A 862 ILE cc_start: 0.8593 (mm) cc_final: 0.8375 (mm) REVERT: A 904 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8319 (pptt) REVERT: A 1043 ASP cc_start: 0.7663 (m-30) cc_final: 0.7308 (m-30) REVERT: A 1126 ARG cc_start: 0.7689 (ptp90) cc_final: 0.7392 (ptp90) REVERT: A 1196 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5212 (pttt) outliers start: 24 outliers final: 4 residues processed: 114 average time/residue: 0.2128 time to fit residues: 33.2323 Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1196 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 94 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A 503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.175876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131289 restraints weight = 10971.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127800 restraints weight = 8077.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128652 restraints weight = 10049.430| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8092 Z= 0.158 Angle : 0.530 13.096 10867 Z= 0.273 Chirality : 0.038 0.160 1160 Planarity : 0.003 0.035 1402 Dihedral : 3.837 46.846 1076 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.80 % Allowed : 22.96 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 949 helix: 1.98 (0.21), residues: 649 sheet: -0.83 (0.95), residues: 32 loop : -1.42 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 850 HIS 0.005 0.001 HIS A 500 PHE 0.018 0.001 PHE A 759 TYR 0.014 0.001 TYR A 755 ARG 0.002 0.000 ARG A1006 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6894 (tt0) REVERT: A 325 MET cc_start: 0.6572 (ttp) cc_final: 0.6141 (ttp) REVERT: A 516 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8200 (mtmt) REVERT: A 862 ILE cc_start: 0.8609 (mm) cc_final: 0.8366 (mm) REVERT: A 904 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8272 (pptt) REVERT: A 1043 ASP cc_start: 0.7551 (m-30) cc_final: 0.7213 (m-30) REVERT: A 1097 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8076 (m) REVERT: A 1126 ARG cc_start: 0.7718 (ptp90) cc_final: 0.7389 (ptp90) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.2075 time to fit residues: 32.6730 Evaluate side-chains 101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A 503 ASN A 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.125717 restraints weight = 10962.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127571 restraints weight = 8087.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128764 restraints weight = 5978.020| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8092 Z= 0.172 Angle : 0.530 12.290 10867 Z= 0.275 Chirality : 0.038 0.175 1160 Planarity : 0.003 0.033 1402 Dihedral : 3.534 24.753 1072 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.91 % Allowed : 23.54 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 949 helix: 2.06 (0.21), residues: 649 sheet: -0.65 (0.97), residues: 32 loop : -1.38 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 850 HIS 0.004 0.001 HIS A 500 PHE 0.018 0.001 PHE A 759 TYR 0.015 0.001 TYR A 755 ARG 0.003 0.000 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6927 (tt0) REVERT: A 516 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8263 (mtmt) REVERT: A 862 ILE cc_start: 0.8591 (mm) cc_final: 0.8327 (mm) REVERT: A 904 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8301 (pptt) REVERT: A 999 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7797 (ttpp) REVERT: A 1043 ASP cc_start: 0.7632 (m-30) cc_final: 0.7324 (m-30) REVERT: A 1097 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8060 (m) REVERT: A 1126 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7468 (ptp90) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.1949 time to fit residues: 31.2506 Evaluate side-chains 105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1210 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A 503 ASN A 837 GLN A1102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128300 restraints weight = 10911.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126139 restraints weight = 9017.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126736 restraints weight = 11791.178| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8092 Z= 0.229 Angle : 0.556 11.807 10867 Z= 0.286 Chirality : 0.039 0.165 1160 Planarity : 0.003 0.031 1402 Dihedral : 3.670 24.919 1072 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.03 % Allowed : 24.36 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 949 helix: 1.95 (0.21), residues: 654 sheet: -0.76 (0.95), residues: 32 loop : -1.32 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 850 HIS 0.004 0.001 HIS A 958 PHE 0.019 0.001 PHE A 759 TYR 0.018 0.001 TYR A 755 ARG 0.003 0.000 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6881 (tt0) REVERT: A 325 MET cc_start: 0.6588 (ttp) cc_final: 0.6163 (ttp) REVERT: A 516 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8369 (mtmt) REVERT: A 760 ILE cc_start: 0.7822 (tp) cc_final: 0.7481 (tt) REVERT: A 862 ILE cc_start: 0.8696 (mm) cc_final: 0.8447 (mm) REVERT: A 999 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7809 (ttpp) REVERT: A 1043 ASP cc_start: 0.7380 (m-30) cc_final: 0.6998 (m-30) REVERT: A 1097 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8180 (m) REVERT: A 1102 ASN cc_start: 0.6648 (OUTLIER) cc_final: 0.6296 (t160) REVERT: A 1126 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7485 (ptp90) outliers start: 26 outliers final: 21 residues processed: 112 average time/residue: 0.2130 time to fit residues: 33.2204 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1210 GLU Chi-restraints excluded: chain A residue 1214 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 0.0470 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 423 HIS ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN A 912 GLN A1102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.175984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127055 restraints weight = 11000.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129516 restraints weight = 8619.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129844 restraints weight = 6723.140| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8092 Z= 0.145 Angle : 0.533 11.676 10867 Z= 0.275 Chirality : 0.037 0.143 1160 Planarity : 0.003 0.033 1402 Dihedral : 3.515 25.364 1072 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.80 % Allowed : 24.71 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.29), residues: 949 helix: 2.16 (0.21), residues: 648 sheet: -0.54 (0.95), residues: 32 loop : -1.28 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 850 HIS 0.008 0.001 HIS A 423 PHE 0.018 0.001 PHE A 759 TYR 0.015 0.001 TYR A 755 ARG 0.003 0.000 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7005 (tt0) REVERT: A 325 MET cc_start: 0.6225 (ttp) cc_final: 0.5811 (ttp) REVERT: A 516 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8316 (mtmt) REVERT: A 564 LYS cc_start: 0.5478 (mtmt) cc_final: 0.5190 (mmmt) REVERT: A 862 ILE cc_start: 0.8576 (mm) cc_final: 0.8302 (mm) REVERT: A 1043 ASP cc_start: 0.7640 (m-30) cc_final: 0.7306 (m-30) REVERT: A 1097 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 1102 ASN cc_start: 0.6604 (OUTLIER) cc_final: 0.6283 (t160) outliers start: 24 outliers final: 15 residues processed: 115 average time/residue: 0.1882 time to fit residues: 30.6795 Evaluate side-chains 104 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1214 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A 496 HIS A 837 GLN A1102 ASN 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 = 0.171329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127400 restraints weight = 11140.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124530 restraints weight = 9104.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125446 restraints weight = 11616.360| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8092 Z= 0.264 Angle : 0.604 11.309 10867 Z= 0.316 Chirality : 0.040 0.154 1160 Planarity : 0.004 0.034 1402 Dihedral : 3.765 25.111 1072 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.15 % Allowed : 24.59 % Favored : 72.26 % 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: 1.43 (0.28), residues: 949 helix: 1.98 (0.21), residues: 642 sheet: -0.75 (0.93), residues: 32 loop : -1.38 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 887 HIS 0.016 0.002 HIS A 496 PHE 0.017 0.002 PHE A 759 TYR 0.020 0.002 TYR A 755 ARG 0.014 0.000 ARG A1126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7017 (tt0) REVERT: A 266 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7964 (ptp-110) REVERT: A 325 MET cc_start: 0.6751 (ttp) cc_final: 0.6246 (ttp) REVERT: A 516 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8409 (mtmt) REVERT: A 518 LYS cc_start: 0.6723 (mmmt) cc_final: 0.6517 (mmtm) REVERT: A 564 LYS cc_start: 0.5461 (mtmt) cc_final: 0.5167 (mmmt) REVERT: A 760 ILE cc_start: 0.7658 (tp) cc_final: 0.7327 (tt) REVERT: A 862 ILE cc_start: 0.8748 (mm) cc_final: 0.8525 (mm) REVERT: A 875 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8370 (mp) REVERT: A 903 MET cc_start: 0.7928 (tpp) cc_final: 0.6616 (mtt) REVERT: A 904 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8306 (pptt) REVERT: A 1043 ASP cc_start: 0.7319 (m-30) cc_final: 0.6932 (m-30) REVERT: A 1097 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (m) outliers start: 27 outliers final: 16 residues processed: 111 average time/residue: 0.2128 time to fit residues: 32.5747 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1214 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 423 HIS A 496 HIS A 837 GLN A1102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.172883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129622 restraints weight = 11198.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127020 restraints weight = 8894.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127866 restraints weight = 11184.794| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8092 Z= 0.207 Angle : 0.566 10.965 10867 Z= 0.296 Chirality : 0.038 0.161 1160 Planarity : 0.003 0.045 1402 Dihedral : 3.666 25.432 1072 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.68 % Allowed : 24.71 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 949 helix: 2.06 (0.21), residues: 642 sheet: -0.64 (0.94), residues: 32 loop : -1.32 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 850 HIS 0.018 0.001 HIS A 496 PHE 0.016 0.001 PHE A 759 TYR 0.018 0.001 TYR A 755 ARG 0.012 0.000 ARG A1126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7099 (tt0) REVERT: A 325 MET cc_start: 0.6424 (ttp) cc_final: 0.6125 (ttp) REVERT: A 661 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6856 (ttm-80) REVERT: A 862 ILE cc_start: 0.8672 (mm) cc_final: 0.8415 (mm) REVERT: A 875 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8307 (mp) REVERT: A 904 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8354 (pptt) REVERT: A 1043 ASP cc_start: 0.7416 (m-30) cc_final: 0.7043 (m-30) REVERT: A 1097 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8200 (m) outliers start: 23 outliers final: 19 residues processed: 106 average time/residue: 0.2166 time to fit residues: 32.2010 Evaluate side-chains 106 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 0.0070 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.0000 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 423 HIS A 496 HIS A1102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131469 restraints weight = 10955.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128551 restraints weight = 8928.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129261 restraints weight = 10757.071| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8092 Z= 0.157 Angle : 0.557 10.946 10867 Z= 0.291 Chirality : 0.037 0.168 1160 Planarity : 0.003 0.045 1402 Dihedral : 3.561 24.422 1072 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.80 % Allowed : 24.48 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.29), residues: 949 helix: 2.14 (0.21), residues: 643 sheet: -0.55 (0.96), residues: 32 loop : -1.27 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 954 HIS 0.021 0.001 HIS A 496 PHE 0.015 0.001 PHE A 759 TYR 0.017 0.001 TYR A 755 ARG 0.011 0.000 ARG A1126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7073 (tt0) REVERT: A 325 MET cc_start: 0.6329 (ttp) cc_final: 0.6072 (ttp) REVERT: A 396 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5678 (pm20) REVERT: A 661 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6859 (ttm-80) REVERT: A 862 ILE cc_start: 0.8623 (mm) cc_final: 0.8369 (mm) REVERT: A 903 MET cc_start: 0.7759 (tpp) cc_final: 0.6501 (mtt) REVERT: A 1043 ASP cc_start: 0.7437 (m-30) cc_final: 0.7081 (m-30) REVERT: A 1097 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8098 (m) REVERT: A 1224 ARG cc_start: 0.7277 (mmm-85) cc_final: 0.6769 (ptp90) outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 0.1844 time to fit residues: 27.1519 Evaluate side-chains 103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.0010 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 423 HIS A 496 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132610 restraints weight = 11114.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129947 restraints weight = 8793.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130763 restraints weight = 10111.149| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8092 Z= 0.153 Angle : 0.555 10.876 10867 Z= 0.289 Chirality : 0.037 0.176 1160 Planarity : 0.003 0.043 1402 Dihedral : 3.486 23.745 1072 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.80 % Allowed : 24.59 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.29), residues: 949 helix: 2.18 (0.21), residues: 643 sheet: -0.52 (0.97), residues: 32 loop : -1.23 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 850 HIS 0.015 0.001 HIS A 496 PHE 0.014 0.001 PHE A 759 TYR 0.016 0.001 TYR A 755 ARG 0.011 0.000 ARG A1126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.25 seconds wall clock time: 42 minutes 41.46 seconds (2561.46 seconds total)