Starting phenix.real_space_refine on Fri Aug 22 20:55:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h4u_34484/08_2025/8h4u_34484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h4u_34484/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h4u_34484/08_2025/8h4u_34484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h4u_34484/08_2025/8h4u_34484.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h4u_34484/08_2025/8h4u_34484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h4u_34484/08_2025/8h4u_34484.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.04, per 1000 atoms: 0.26 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: 0.63 Conformation dependent library (CDL) restraints added in 402.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.31 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: 1.29 Time building geometry restraints manager: 0.86 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- 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= 0.117 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (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 ARG 0.002 0.000 ARG A 672 TYR 0.015 0.001 TYR A 282 PHE 0.012 0.001 PHE A 882 TRP 0.011 0.001 TRP A 619 HIS 0.008 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8092) covalent geometry : angle 0.59340 (10867) hydrogen bonds : bond 0.27047 ( 447) hydrogen bonds : angle 6.17481 ( 1314) *********************** 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 : 0.270 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: 0.0819 time to fit residues: 11.6414 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 : 0.274 ------------------------------------------------------------------------------- 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 49 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 697 ASN A 712 HIS A 775 HIS A 837 GLN A 905 ASN A1168 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.176048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130524 restraints weight = 10971.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128376 restraints weight = 8937.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129505 restraints weight = 10648.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130209 restraints weight = 6758.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131206 restraints weight = 6085.996| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8092 Z= 0.142 Angle : 0.575 10.900 10867 Z= 0.304 Chirality : 0.039 0.149 1160 Planarity : 0.004 0.035 1402 Dihedral : 4.891 60.127 1083 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.56 % Allowed : 23.19 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.28), residues: 949 helix: 1.60 (0.21), residues: 648 sheet: -1.05 (0.97), residues: 32 loop : -1.60 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.013 0.001 TYR A 755 PHE 0.028 0.001 PHE A 283 TRP 0.012 0.001 TRP A 959 HIS 0.008 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8092) covalent geometry : angle 0.57548 (10867) hydrogen bonds : bond 0.05881 ( 447) hydrogen bonds : angle 3.87053 ( 1314) *********************** 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: 22 poor density : 101 time to evaluate : 0.329 Fit side-chains REVERT: A 904 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8272 (pptt) REVERT: A 1006 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8096 (mtt-85) REVERT: A 1043 ASP cc_start: 0.7645 (m-30) cc_final: 0.7255 (m-30) REVERT: A 1196 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5158 (pttm) outliers start: 22 outliers final: 8 residues processed: 119 average time/residue: 0.0825 time to fit residues: 13.5755 Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 503 ASN 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 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 34 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130785 restraints weight = 10888.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130499 restraints weight = 9262.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131677 restraints weight = 8014.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132415 restraints weight = 6040.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132984 restraints weight = 5697.215| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2145 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= 0.128 Angle : 0.557 14.965 10867 Z= 0.287 Chirality : 0.038 0.147 1160 Planarity : 0.003 0.036 1402 Dihedral : 4.032 57.415 1076 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.28), residues: 949 helix: 1.89 (0.21), residues: 648 sheet: -0.94 (0.95), residues: 32 loop : -1.50 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1224 TYR 0.015 0.001 TYR A 755 PHE 0.018 0.001 PHE A 759 TRP 0.028 0.001 TRP A 850 HIS 0.005 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8092) covalent geometry : angle 0.55715 (10867) hydrogen bonds : bond 0.05088 ( 447) hydrogen bonds : angle 3.61609 ( 1314) *********************** 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 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 516 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8218 (mtmt) REVERT: A 731 MET cc_start: 0.3765 (ttt) cc_final: 0.3497 (ttm) REVERT: A 862 ILE cc_start: 0.8607 (mm) cc_final: 0.8364 (mm) REVERT: A 904 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8266 (pptt) REVERT: A 1043 ASP cc_start: 0.7527 (m-30) cc_final: 0.7168 (m-30) REVERT: A 1196 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5136 (pttt) outliers start: 24 outliers final: 8 residues processed: 112 average time/residue: 0.0916 time to fit residues: 14.2184 Evaluate side-chains 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1108 LEU 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 33 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.174779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130226 restraints weight = 11078.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128366 restraints weight = 10670.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129329 restraints weight = 10615.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131727 restraints weight = 7184.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132004 restraints weight = 5891.916| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2381 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= 0.129 Angle : 0.543 12.994 10867 Z= 0.279 Chirality : 0.038 0.147 1160 Planarity : 0.003 0.034 1402 Dihedral : 3.943 49.665 1076 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.38 % Allowed : 21.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.28), residues: 949 helix: 1.97 (0.21), residues: 649 sheet: -0.83 (0.95), residues: 32 loop : -1.43 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1006 TYR 0.016 0.001 TYR A 755 PHE 0.018 0.001 PHE A 759 TRP 0.012 0.001 TRP A 850 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8092) covalent geometry : angle 0.54253 (10867) hydrogen bonds : bond 0.04746 ( 447) hydrogen bonds : angle 3.50022 ( 1314) *********************** 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 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.6470 (ttp) cc_final: 0.6003 (ttp) REVERT: A 516 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8315 (mtmt) REVERT: A 731 MET cc_start: 0.4024 (ttt) cc_final: 0.3818 (ttm) REVERT: A 862 ILE cc_start: 0.8606 (mm) cc_final: 0.8361 (mm) REVERT: A 904 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8267 (pptt) REVERT: A 1043 ASP cc_start: 0.7485 (m-30) cc_final: 0.7079 (m-30) REVERT: A 1097 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8122 (m) REVERT: A 1196 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5112 (pttt) outliers start: 29 outliers final: 15 residues processed: 114 average time/residue: 0.0834 time to fit residues: 13.3344 Evaluate side-chains 101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 576 ILE 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 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 1196 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 92 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128706 restraints weight = 10953.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133864 restraints weight = 8662.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132847 restraints weight = 5413.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132717 restraints weight = 4670.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132897 restraints weight = 4614.676| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2668 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= 0.100 Angle : 0.513 12.245 10867 Z= 0.266 Chirality : 0.037 0.176 1160 Planarity : 0.003 0.034 1402 Dihedral : 3.690 39.944 1076 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.10 % Allowed : 23.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.29), residues: 949 helix: 2.14 (0.21), residues: 650 sheet: -0.42 (0.99), residues: 32 loop : -1.29 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1126 TYR 0.014 0.001 TYR A 755 PHE 0.020 0.001 PHE A 759 TRP 0.009 0.001 TRP A 850 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8092) covalent geometry : angle 0.51325 (10867) hydrogen bonds : bond 0.03829 ( 447) hydrogen bonds : angle 3.31425 ( 1314) *********************** 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 123 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6916 (tt0) REVERT: A 325 MET cc_start: 0.6096 (ttp) cc_final: 0.5713 (ttp) REVERT: A 516 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8343 (mtmt) REVERT: A 567 THR cc_start: 0.8087 (t) cc_final: 0.7650 (m) REVERT: A 862 ILE cc_start: 0.8504 (mm) cc_final: 0.8224 (mm) REVERT: A 904 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8135 (pptt) REVERT: A 999 LYS cc_start: 0.8335 (ttpp) cc_final: 0.7909 (ttpp) REVERT: A 1043 ASP cc_start: 0.7674 (m-30) cc_final: 0.7323 (m-30) REVERT: A 1097 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7927 (m) outliers start: 18 outliers final: 10 residues processed: 114 average time/residue: 0.0817 time to fit residues: 13.1001 Evaluate side-chains 100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 503 ASN A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.170028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125713 restraints weight = 11063.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123615 restraints weight = 10084.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124389 restraints weight = 11832.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125331 restraints weight = 7205.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128303 restraints weight = 6246.880| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8092 Z= 0.225 Angle : 0.627 11.197 10867 Z= 0.324 Chirality : 0.042 0.170 1160 Planarity : 0.004 0.040 1402 Dihedral : 3.970 24.206 1072 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.15 % Allowed : 23.89 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.28), residues: 949 helix: 1.79 (0.21), residues: 646 sheet: -1.14 (0.93), residues: 33 loop : -1.37 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1126 TYR 0.023 0.002 TYR A 755 PHE 0.041 0.002 PHE A 283 TRP 0.014 0.002 TRP A 887 HIS 0.009 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8092) covalent geometry : angle 0.62684 (10867) hydrogen bonds : bond 0.05875 ( 447) hydrogen bonds : angle 3.70602 ( 1314) *********************** 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: 27 poor density : 97 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 516 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8445 (mtmt) REVERT: A 760 ILE cc_start: 0.7813 (tp) cc_final: 0.7471 (tt) REVERT: A 904 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8350 (pptt) REVERT: A 961 VAL cc_start: 0.8314 (m) cc_final: 0.8058 (p) REVERT: A 1043 ASP cc_start: 0.7396 (m-30) cc_final: 0.7030 (m-30) REVERT: A 1097 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8317 (m) outliers start: 27 outliers final: 20 residues processed: 116 average time/residue: 0.0824 time to fit residues: 13.0971 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 360 VAL 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 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 787 ARG 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 1053 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A1102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131322 restraints weight = 10977.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128009 restraints weight = 8991.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129420 restraints weight = 9191.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129879 restraints weight = 7088.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130578 restraints weight = 6940.920| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8092 Z= 0.109 Angle : 0.541 11.379 10867 Z= 0.277 Chirality : 0.037 0.144 1160 Planarity : 0.003 0.041 1402 Dihedral : 3.670 26.141 1072 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.91 % Allowed : 23.89 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.29), residues: 949 helix: 2.10 (0.21), residues: 649 sheet: -0.61 (0.96), residues: 32 loop : -1.29 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1126 TYR 0.016 0.001 TYR A 755 PHE 0.035 0.001 PHE A 283 TRP 0.006 0.001 TRP A 954 HIS 0.007 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8092) covalent geometry : angle 0.54144 (10867) hydrogen bonds : bond 0.04072 ( 447) hydrogen bonds : angle 3.32767 ( 1314) *********************** 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 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.6431 (ttp) cc_final: 0.6107 (ttp) REVERT: A 731 MET cc_start: 0.4285 (ttm) cc_final: 0.3511 (ttm) REVERT: A 862 ILE cc_start: 0.8622 (mm) cc_final: 0.8365 (mm) REVERT: A 903 MET cc_start: 0.7724 (tpp) cc_final: 0.6462 (mtt) REVERT: A 961 VAL cc_start: 0.8196 (m) cc_final: 0.7983 (p) REVERT: A 1043 ASP cc_start: 0.7570 (m-30) cc_final: 0.7199 (m-30) REVERT: A 1097 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8124 (m) outliers start: 25 outliers final: 16 residues processed: 110 average time/residue: 0.0927 time to fit residues: 14.1261 Evaluate side-chains 100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 423 HIS 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 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 1099 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 36 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8264 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.175031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131304 restraints weight = 11088.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127929 restraints weight = 9459.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128817 restraints weight = 12933.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129756 restraints weight = 8019.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130434 restraints weight = 7008.269| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8092 Z= 0.118 Angle : 0.550 10.997 10867 Z= 0.287 Chirality : 0.037 0.152 1160 Planarity : 0.003 0.035 1402 Dihedral : 3.560 24.842 1072 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.56 % Allowed : 24.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.29), residues: 949 helix: 2.14 (0.21), residues: 649 sheet: -0.51 (0.96), residues: 32 loop : -1.26 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1173 TYR 0.017 0.001 TYR A 755 PHE 0.016 0.001 PHE A 759 TRP 0.006 0.001 TRP A 954 HIS 0.005 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8092) covalent geometry : angle 0.55029 (10867) hydrogen bonds : bond 0.04212 ( 447) hydrogen bonds : angle 3.35124 ( 1314) *********************** 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 109 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.6275 (ttp) cc_final: 0.5977 (ttp) REVERT: A 564 LYS cc_start: 0.5519 (mtmt) cc_final: 0.5259 (mmmt) REVERT: A 567 THR cc_start: 0.8107 (t) cc_final: 0.7719 (m) REVERT: A 862 ILE cc_start: 0.8628 (mm) cc_final: 0.8386 (mm) REVERT: A 903 MET cc_start: 0.7708 (tpp) cc_final: 0.6489 (mtt) REVERT: A 904 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8338 (pptt) REVERT: A 961 VAL cc_start: 0.8115 (m) cc_final: 0.7910 (p) REVERT: A 1043 ASP cc_start: 0.7543 (m-30) cc_final: 0.7169 (m-30) REVERT: A 1097 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 1126 ARG cc_start: 0.7535 (mtp-110) cc_final: 0.7305 (mtm-85) outliers start: 22 outliers final: 15 residues processed: 103 average time/residue: 0.0848 time to fit residues: 12.1459 Evaluate side-chains 99 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 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 1110 VAL Chi-restraints excluded: chain A residue 1210 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.171226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121507 restraints weight = 11055.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124235 restraints weight = 8932.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124596 restraints weight = 6142.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123882 restraints weight = 5153.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124583 restraints weight = 5742.925| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8092 Z= 0.189 Angle : 0.599 10.697 10867 Z= 0.310 Chirality : 0.040 0.172 1160 Planarity : 0.004 0.046 1402 Dihedral : 3.859 25.478 1072 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.80 % Allowed : 24.24 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.28), residues: 949 helix: 1.90 (0.21), residues: 648 sheet: -0.95 (0.94), residues: 33 loop : -1.21 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1173 TYR 0.022 0.002 TYR A 755 PHE 0.015 0.002 PHE A 759 TRP 0.012 0.001 TRP A 887 HIS 0.006 0.001 HIS A 958 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8092) covalent geometry : angle 0.59939 (10867) hydrogen bonds : bond 0.05263 ( 447) hydrogen bonds : angle 3.54824 ( 1314) *********************** 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 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.6413 (ttp) cc_final: 0.6051 (ttp) REVERT: A 564 LYS cc_start: 0.5603 (mtmt) cc_final: 0.5379 (mmmt) REVERT: A 578 MET cc_start: 0.6122 (ppp) cc_final: 0.5791 (ptp) REVERT: A 661 ARG cc_start: 0.7155 (ttm170) cc_final: 0.6820 (ttm-80) REVERT: A 760 ILE cc_start: 0.7839 (tp) cc_final: 0.7505 (tt) REVERT: A 862 ILE cc_start: 0.8685 (mm) cc_final: 0.8439 (mm) REVERT: A 904 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8363 (pptt) REVERT: A 961 VAL cc_start: 0.8205 (m) cc_final: 0.7969 (p) REVERT: A 1043 ASP cc_start: 0.7601 (m-30) cc_final: 0.7289 (m-30) REVERT: A 1097 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8263 (m) outliers start: 24 outliers final: 17 residues processed: 105 average time/residue: 0.0898 time to fit residues: 13.0731 Evaluate side-chains 104 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 360 VAL Chi-restraints excluded: chain A residue 500 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 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 Chi-restraints excluded: chain A residue 1210 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 503 ASN A1102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129250 restraints weight = 11019.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127056 restraints weight = 8958.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127961 restraints weight = 10033.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129171 restraints weight = 7072.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129633 restraints weight = 6170.380| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3265 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= 0.127 Angle : 0.570 12.210 10867 Z= 0.295 Chirality : 0.038 0.179 1160 Planarity : 0.003 0.040 1402 Dihedral : 3.687 25.352 1072 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.21 % Allowed : 25.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.29), residues: 949 helix: 2.08 (0.21), residues: 643 sheet: -0.63 (0.95), residues: 32 loop : -1.26 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1173 TYR 0.019 0.001 TYR A 755 PHE 0.018 0.001 PHE A 620 TRP 0.007 0.001 TRP A 954 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8092) covalent geometry : angle 0.56976 (10867) hydrogen bonds : bond 0.04418 ( 447) hydrogen bonds : angle 3.44413 ( 1314) ********************** 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 106 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 289 TYR cc_start: 0.7667 (t80) cc_final: 0.7432 (t80) REVERT: A 325 MET cc_start: 0.6317 (ttp) cc_final: 0.5991 (ttp) REVERT: A 567 THR cc_start: 0.8119 (t) cc_final: 0.7734 (m) REVERT: A 578 MET cc_start: 0.6094 (ppp) cc_final: 0.5555 (ptp) REVERT: A 661 ARG cc_start: 0.7145 (ttm170) cc_final: 0.6801 (ttm-80) REVERT: A 862 ILE cc_start: 0.8629 (mm) cc_final: 0.8369 (mm) REVERT: A 903 MET cc_start: 0.7940 (tpp) cc_final: 0.6649 (mtt) REVERT: A 961 VAL cc_start: 0.8124 (m) cc_final: 0.7839 (p) REVERT: A 1043 ASP cc_start: 0.7565 (m-30) cc_final: 0.7177 (m-30) REVERT: A 1097 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (m) outliers start: 19 outliers final: 17 residues processed: 101 average time/residue: 0.0768 time to fit residues: 10.8756 Evaluate side-chains 101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 500 HIS 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 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 1099 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129518 restraints weight = 11104.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126770 restraints weight = 9214.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127859 restraints weight = 11371.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128729 restraints weight = 7121.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131365 restraints weight = 6258.742| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 8092 Z= 0.216 Angle : 1.040 59.198 10867 Z= 0.621 Chirality : 0.048 0.754 1160 Planarity : 0.007 0.166 1402 Dihedral : 3.929 42.161 1072 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.10 % Allowed : 24.71 % Favored : 73.19 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.29), residues: 949 helix: 2.05 (0.21), residues: 643 sheet: -0.63 (0.96), residues: 32 loop : -1.31 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1126 TYR 0.018 0.001 TYR A 755 PHE 0.013 0.001 PHE A 759 TRP 0.006 0.001 TRP A 954 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8092) covalent geometry : angle 1.04008 (10867) hydrogen bonds : bond 0.04507 ( 447) hydrogen bonds : angle 3.44749 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1269.29 seconds wall clock time: 22 minutes 36.73 seconds (1356.73 seconds total)