Starting phenix.real_space_refine on Wed Mar 12 12:40:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h4u_34484/03_2025/8h4u_34484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h4u_34484/03_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_34484/03_2025/8h4u_34484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h4u_34484/03_2025/8h4u_34484.map" model { file = "/net/cci-nas-00/data/ceres_data/8h4u_34484/03_2025/8h4u_34484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h4u_34484/03_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.02, per 1000 atoms: 0.76 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: 2.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.83 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: 2.28 Time building geometry restraints manager: 3.15 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: 0.920 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.110 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- 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 : 0.850 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: 0.1895 time to fit residues: 26.9042 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 : 0.869 ------------------------------------------------------------------------------- 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 = 10903.078| |-----------------------------------------------------------------------------| 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 : 1.023 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: 0.8010 (mmt180) REVERT: A 1043 ASP cc_start: 0.7615 (m-30) cc_final: 0.7257 (m-30) REVERT: A 1089 GLU cc_start: 0.7491 (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: 0.2127 time to fit residues: 35.0000 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 : 0.961 ------------------------------------------------------------------------------- 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: 9.9990 chunk 11 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 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: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.175374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131150 restraints weight = 10937.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128699 restraints weight = 9307.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129878 restraints weight = 9836.470| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8092 Z= 0.155 Angle : 0.549 15.080 10867 Z= 0.282 Chirality : 0.038 0.222 1160 Planarity : 0.003 0.034 1402 Dihedral : 3.982 55.085 1076 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.68 % Allowed : 23.19 % 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: 1.30 (0.28), residues: 949 helix: 1.88 (0.21), residues: 648 sheet: -1.00 (0.94), 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 0.019 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 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 516 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8178 (mtmt) REVERT: A 731 MET cc_start: 0.3999 (ttt) cc_final: 0.3755 (ttm) REVERT: A 862 ILE cc_start: 0.8576 (mm) cc_final: 0.8356 (mm) REVERT: A 904 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8303 (pptt) REVERT: A 1043 ASP cc_start: 0.7601 (m-30) cc_final: 0.7246 (m-30) REVERT: A 1126 ARG cc_start: 0.7670 (ptp90) cc_final: 0.7369 (ptp90) REVERT: A 1196 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5181 (pttt) outliers start: 23 outliers final: 4 residues processed: 113 average time/residue: 0.2557 time to fit residues: 41.8370 Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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: 0.0470 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.176088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131595 restraints weight = 10915.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130770 restraints weight = 8091.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131451 restraints weight = 9015.708| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2490 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= 0.150 Angle : 0.527 13.047 10867 Z= 0.271 Chirality : 0.037 0.165 1160 Planarity : 0.003 0.034 1402 Dihedral : 3.810 47.721 1076 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.80 % Allowed : 22.49 % Favored : 74.71 % 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: 1.49 (0.29), residues: 949 helix: 2.02 (0.21), residues: 649 sheet: -0.76 (0.96), residues: 32 loop : -1.43 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 850 HIS 0.005 0.001 HIS A 500 PHE 0.018 0.001 PHE A 759 TYR 0.013 0.001 TYR A 755 ARG 0.002 0.000 ARG A1224 *********************** 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 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6883 (tt0) REVERT: A 325 MET cc_start: 0.6357 (ttp) cc_final: 0.5955 (ttp) REVERT: A 516 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8169 (mtmt) REVERT: A 862 ILE cc_start: 0.8582 (mm) cc_final: 0.8333 (mm) REVERT: A 904 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8166 (pptt) REVERT: A 1043 ASP cc_start: 0.7554 (m-30) cc_final: 0.7199 (m-30) REVERT: A 1097 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8016 (m) REVERT: A 1126 ARG cc_start: 0.7674 (ptp90) cc_final: 0.7349 (ptp90) outliers start: 24 outliers final: 12 residues processed: 111 average time/residue: 0.2767 time to fit residues: 43.1316 Evaluate side-chains 99 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.5980 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.173693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123895 restraints weight = 11036.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125016 restraints weight = 8773.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126136 restraints weight = 6696.889| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2683 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= 0.218 Angle : 0.559 12.169 10867 Z= 0.290 Chirality : 0.039 0.180 1160 Planarity : 0.003 0.032 1402 Dihedral : 3.658 24.459 1072 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.80 % Allowed : 23.78 % Favored : 73.43 % 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: 1.46 (0.29), residues: 949 helix: 2.00 (0.21), residues: 648 sheet: -0.73 (0.97), residues: 32 loop : -1.44 (0.37), residues: 269 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 0.019 0.002 PHE A 759 TYR 0.018 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 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6879 (tt0) REVERT: A 516 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8321 (mtmt) REVERT: A 760 ILE cc_start: 0.7885 (tp) cc_final: 0.7499 (tt) REVERT: A 862 ILE cc_start: 0.8646 (mm) cc_final: 0.8403 (mm) REVERT: A 903 MET cc_start: 0.7874 (tpp) cc_final: 0.6437 (mtt) REVERT: A 904 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8273 (pptt) REVERT: A 999 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7751 (ttpp) REVERT: A 1043 ASP cc_start: 0.7624 (m-30) cc_final: 0.7318 (m-30) REVERT: A 1097 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8185 (m) REVERT: A 1126 ARG cc_start: 0.7771 (ptp90) cc_final: 0.7505 (ptp90) outliers start: 24 outliers final: 17 residues processed: 111 average time/residue: 0.1877 time to fit residues: 29.6306 Evaluate side-chains 105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1214 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 50.0000 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 A 912 GLN A1058 GLN A1102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131089 restraints weight = 10858.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128227 restraints weight = 8460.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129275 restraints weight = 10895.611| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8092 Z= 0.144 Angle : 0.521 11.857 10867 Z= 0.269 Chirality : 0.037 0.186 1160 Planarity : 0.003 0.033 1402 Dihedral : 3.517 24.320 1072 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.91 % Allowed : 24.36 % 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: 1.65 (0.29), residues: 949 helix: 2.12 (0.21), residues: 648 sheet: -0.54 (0.97), residues: 32 loop : -1.33 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 850 HIS 0.004 0.001 HIS A 497 PHE 0.019 0.001 PHE A 759 TYR 0.015 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 124 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7016 (tt0) REVERT: A 516 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8325 (mtmt) REVERT: A 567 THR cc_start: 0.8172 (t) cc_final: 0.7751 (m) REVERT: A 760 ILE cc_start: 0.7809 (tp) cc_final: 0.7450 (tt) REVERT: A 862 ILE cc_start: 0.8599 (mm) cc_final: 0.8339 (mm) REVERT: A 904 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8332 (pptt) REVERT: A 1043 ASP cc_start: 0.7429 (m-30) cc_final: 0.7058 (m-30) REVERT: A 1097 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8083 (m) REVERT: A 1126 ARG cc_start: 0.7715 (ptp90) cc_final: 0.7472 (ptp90) REVERT: A 1177 GLU cc_start: 0.5854 (tm-30) cc_final: 0.5650 (tm-30) outliers start: 25 outliers final: 20 residues processed: 117 average time/residue: 0.1859 time to fit residues: 30.5678 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 320 LEU 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 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 1110 VAL Chi-restraints excluded: chain A residue 1210 GLU 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: 0.0570 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 88 optimal weight: 0.0970 chunk 46 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- 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 A1102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134732 restraints weight = 11000.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132860 restraints weight = 8328.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134133 restraints weight = 8997.121| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3109 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= 0.131 Angle : 0.523 11.700 10867 Z= 0.272 Chirality : 0.037 0.207 1160 Planarity : 0.003 0.033 1402 Dihedral : 3.387 24.217 1072 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.80 % Allowed : 24.94 % 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: 1.87 (0.29), residues: 949 helix: 2.28 (0.21), residues: 651 sheet: -0.40 (0.97), residues: 32 loop : -1.27 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 850 HIS 0.006 0.001 HIS A 423 PHE 0.017 0.001 PHE A 759 TYR 0.013 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 125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6974 (tt0) REVERT: A 267 GLU cc_start: 0.8017 (pm20) cc_final: 0.7787 (tp30) REVERT: A 325 MET cc_start: 0.5950 (ttp) cc_final: 0.5603 (ttp) REVERT: A 567 THR cc_start: 0.8096 (t) cc_final: 0.7674 (m) REVERT: A 862 ILE cc_start: 0.8554 (mm) cc_final: 0.8276 (mm) REVERT: A 903 MET cc_start: 0.7643 (tpp) cc_final: 0.6391 (mtt) REVERT: A 904 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8193 (pptt) REVERT: A 1043 ASP cc_start: 0.7491 (m-30) cc_final: 0.7149 (m-30) REVERT: A 1097 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7859 (m) REVERT: A 1113 ASP cc_start: 0.8245 (m-30) cc_final: 0.7962 (m-30) outliers start: 24 outliers final: 15 residues processed: 117 average time/residue: 0.2071 time to fit residues: 33.4269 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 500 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 942 SER 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 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 503 ASN A 837 GLN ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130227 restraints weight = 11097.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127694 restraints weight = 9000.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129003 restraints weight = 8575.527| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8092 Z= 0.201 Angle : 0.571 11.173 10867 Z= 0.295 Chirality : 0.038 0.193 1160 Planarity : 0.004 0.038 1402 Dihedral : 3.496 23.414 1072 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.33 % Allowed : 24.94 % 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: 1.81 (0.29), residues: 949 helix: 2.26 (0.21), residues: 643 sheet: -0.48 (0.96), residues: 32 loop : -1.24 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 850 HIS 0.017 0.002 HIS A 496 PHE 0.017 0.001 PHE A 759 TYR 0.017 0.001 TYR A 755 ARG 0.013 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 111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7038 (tt0) REVERT: A 325 MET cc_start: 0.6234 (ttp) cc_final: 0.5884 (ttp) REVERT: A 564 LYS cc_start: 0.5565 (mtmt) cc_final: 0.5246 (mmmt) REVERT: A 862 ILE cc_start: 0.8665 (mm) cc_final: 0.8420 (mm) REVERT: A 904 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8341 (pptt) REVERT: A 1043 ASP cc_start: 0.7441 (m-30) cc_final: 0.7031 (m-30) REVERT: A 1097 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8093 (m) outliers start: 20 outliers final: 16 residues processed: 105 average time/residue: 0.1904 time to fit residues: 28.4239 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 : 1.007 ------------------------------------------------------------------------------- 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 496 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 930 SER Chi-restraints excluded: chain A residue 942 SER 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 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 8.9990 chunk 71 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 503 ASN A 837 GLN A1102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130981 restraints weight = 11129.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127643 restraints weight = 8743.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128358 restraints weight = 10736.469| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8092 Z= 0.166 Angle : 0.554 11.178 10867 Z= 0.284 Chirality : 0.038 0.196 1160 Planarity : 0.004 0.046 1402 Dihedral : 3.489 24.809 1072 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.33 % Allowed : 24.83 % Favored : 72.84 % 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: 1.80 (0.29), residues: 949 helix: 2.26 (0.21), residues: 643 sheet: -0.48 (0.96), residues: 32 loop : -1.26 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 850 HIS 0.013 0.001 HIS A 496 PHE 0.016 0.001 PHE A 759 TYR 0.016 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 111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7063 (tt0) REVERT: A 325 MET cc_start: 0.6207 (ttp) cc_final: 0.5892 (ttp) REVERT: A 564 LYS cc_start: 0.5509 (mtmt) cc_final: 0.5275 (mmmt) REVERT: A 862 ILE cc_start: 0.8654 (mm) cc_final: 0.8402 (mm) REVERT: A 903 MET cc_start: 0.7850 (tpp) cc_final: 0.6330 (mtt) REVERT: A 904 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8378 (pptt) REVERT: A 1043 ASP cc_start: 0.7446 (m-30) cc_final: 0.7049 (m-30) REVERT: A 1097 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8062 (m) REVERT: A 1177 GLU cc_start: 0.6025 (tm-30) cc_final: 0.5421 (tm-30) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.1850 time to fit residues: 28.0075 Evaluate side-chains 102 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 320 LEU 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 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 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 46 optimal weight: 0.0770 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 503 ASN A1102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132971 restraints weight = 10981.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130005 restraints weight = 8834.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130941 restraints weight = 10164.529| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3311 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= 0.147 Angle : 0.544 11.157 10867 Z= 0.280 Chirality : 0.037 0.195 1160 Planarity : 0.004 0.045 1402 Dihedral : 3.429 22.889 1072 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.33 % Allowed : 24.59 % Favored : 73.08 % 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: 1.89 (0.29), residues: 949 helix: 2.31 (0.21), residues: 644 sheet: -0.45 (0.97), residues: 32 loop : -1.20 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 850 HIS 0.023 0.001 HIS A 496 PHE 0.016 0.001 PHE A 759 TYR 0.016 0.001 TYR A 755 ARG 0.012 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 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7097 (tt0) REVERT: A 325 MET cc_start: 0.6168 (ttp) cc_final: 0.5826 (ttp) REVERT: A 564 LYS cc_start: 0.5549 (mtmt) cc_final: 0.5273 (mmmt) REVERT: A 567 THR cc_start: 0.8058 (t) cc_final: 0.7663 (m) REVERT: A 578 MET cc_start: 0.6134 (ppp) cc_final: 0.5336 (ptp) REVERT: A 862 ILE cc_start: 0.8632 (mm) cc_final: 0.8366 (mm) REVERT: A 904 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8315 (pptt) REVERT: A 1043 ASP cc_start: 0.7297 (m-30) cc_final: 0.6851 (m-30) REVERT: A 1097 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7967 (m) REVERT: A 1177 GLU cc_start: 0.5960 (tm-30) cc_final: 0.5424 (tm-30) outliers start: 20 outliers final: 15 residues processed: 101 average time/residue: 0.1903 time to fit residues: 27.3392 Evaluate side-chains 102 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 496 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 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 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 496 HIS A 503 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133084 restraints weight = 11130.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131376 restraints weight = 9173.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132396 restraints weight = 10675.273| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8092 Z= 0.156 Angle : 0.548 11.094 10867 Z= 0.281 Chirality : 0.037 0.182 1160 Planarity : 0.004 0.042 1402 Dihedral : 3.451 24.294 1072 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.10 % Allowed : 25.06 % Favored : 72.84 % 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: 1.90 (0.29), residues: 949 helix: 2.31 (0.21), residues: 644 sheet: -0.43 (0.97), residues: 32 loop : -1.19 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 850 HIS 0.021 0.001 HIS A 496 PHE 0.015 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: 2484.23 seconds wall clock time: 44 minutes 33.86 seconds (2673.86 seconds total)