Starting phenix.real_space_refine on Sat Dec 28 05:48:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h4u_34484/12_2024/8h4u_34484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h4u_34484/12_2024/8h4u_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_34484/12_2024/8h4u_34484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h4u_34484/12_2024/8h4u_34484.map" model { file = "/net/cci-nas-00/data/ceres_data/8h4u_34484/12_2024/8h4u_34484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h4u_34484/12_2024/8h4u_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7944 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7944 Classifications: {'peptide': 959} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 932} Chain breaks: 4 Time building chain proxies: 4.88, per 1000 atoms: 0.61 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 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: 0.89 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: 2.36 Time building geometry restraints manager: 2.35 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: 0.470 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- 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 : 0.887 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: 0.1872 time to fit residues: 26.5081 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 : 0.947 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8092 Z= 0.277 Angle : 0.617 11.693 10867 Z= 0.323 Chirality : 0.041 0.154 1160 Planarity : 0.004 0.036 1402 Dihedral : 5.077 62.871 1083 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.03 % Allowed : 23.19 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.28), residues: 949 helix: 1.45 (0.21), residues: 646 sheet: -1.46 (0.93), residues: 33 loop : -1.60 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 959 HIS 0.007 0.002 HIS A 500 PHE 0.029 0.002 PHE A 283 TYR 0.014 0.002 TYR A 755 ARG 0.003 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.951 Fit side-chains REVERT: A 904 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8325 (pptt) REVERT: A 1006 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7981 (mmt180) REVERT: A 1043 ASP cc_start: 0.7582 (m-30) cc_final: 0.7243 (m-30) REVERT: A 1196 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5138 (pttt) outliers start: 26 outliers final: 11 residues processed: 118 average time/residue: 0.2001 time to fit residues: 32.7466 Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 A1168 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8092 Z= 0.217 Angle : 0.577 14.664 10867 Z= 0.297 Chirality : 0.039 0.212 1160 Planarity : 0.003 0.034 1402 Dihedral : 4.123 54.266 1076 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.03 % Allowed : 23.08 % 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: 1.11 (0.28), residues: 949 helix: 1.73 (0.21), residues: 648 sheet: -1.23 (0.91), residues: 32 loop : -1.52 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 850 HIS 0.005 0.001 HIS A 500 PHE 0.019 0.002 PHE A 283 TYR 0.016 0.001 TYR A 755 ARG 0.003 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 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 516 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8272 (mtmt) REVERT: A 760 ILE cc_start: 0.7811 (tp) cc_final: 0.7499 (tt) REVERT: A 904 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8343 (pptt) REVERT: A 1006 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8058 (mmt180) REVERT: A 1043 ASP cc_start: 0.7555 (m-30) cc_final: 0.7225 (m-30) REVERT: A 1126 ARG cc_start: 0.7643 (ptp90) cc_final: 0.7417 (ptp90) REVERT: A 1196 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.5264 (pttt) outliers start: 26 outliers final: 10 residues processed: 109 average time/residue: 0.2196 time to fit residues: 32.8057 Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU 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 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1154 MET 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 85 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A 503 ASN A 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8092 Z= 0.242 Angle : 0.572 12.800 10867 Z= 0.296 Chirality : 0.039 0.157 1160 Planarity : 0.003 0.033 1402 Dihedral : 4.052 43.581 1076 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.61 % Allowed : 22.96 % 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: 1.14 (0.28), residues: 949 helix: 1.70 (0.21), residues: 655 sheet: -1.18 (0.91), residues: 32 loop : -1.43 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 850 HIS 0.004 0.001 HIS A 500 PHE 0.018 0.002 PHE A 759 TYR 0.017 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 123 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6882 (tt0) REVERT: A 347 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8580 (mp) REVERT: A 516 LYS cc_start: 0.8529 (mtmt) cc_final: 0.8316 (mtmt) REVERT: A 760 ILE cc_start: 0.7870 (tp) cc_final: 0.7555 (tt) REVERT: A 904 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8353 (pptt) REVERT: A 999 LYS cc_start: 0.8358 (ttpp) cc_final: 0.7970 (ttpp) REVERT: A 1006 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8110 (mmt180) REVERT: A 1043 ASP cc_start: 0.7597 (m-30) cc_final: 0.7275 (m-30) REVERT: A 1097 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8282 (m) REVERT: A 1126 ARG cc_start: 0.7691 (ptp90) cc_final: 0.7457 (ptp90) REVERT: A 1224 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.6831 (ttm110) outliers start: 31 outliers final: 19 residues processed: 115 average time/residue: 0.2189 time to fit residues: 34.0922 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 360 VAL 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 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 1006 ARG 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 1188 THR Chi-restraints excluded: chain A residue 1214 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2672 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= 0.154 Angle : 0.533 12.422 10867 Z= 0.276 Chirality : 0.038 0.178 1160 Planarity : 0.003 0.033 1402 Dihedral : 3.620 25.259 1072 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.03 % Allowed : 24.59 % Favored : 72.38 % 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: 1.98 (0.21), residues: 648 sheet: -0.66 (0.96), residues: 32 loop : -1.40 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 850 HIS 0.004 0.001 HIS A 500 PHE 0.017 0.001 PHE A 759 TYR 0.015 0.001 TYR A 289 ARG 0.002 0.000 ARG A1224 *********************** 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: 26 poor density : 97 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6891 (tt0) REVERT: A 516 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8362 (mtmt) REVERT: A 692 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6836 (mptt) REVERT: A 760 ILE cc_start: 0.7780 (tp) cc_final: 0.7489 (tt) REVERT: A 904 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8348 (pptt) REVERT: A 999 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7850 (ttpp) REVERT: A 1043 ASP cc_start: 0.7553 (m-30) cc_final: 0.7205 (m-30) REVERT: A 1097 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8157 (m) REVERT: A 1126 ARG cc_start: 0.7649 (ptp90) cc_final: 0.7445 (ptp90) outliers start: 26 outliers final: 17 residues processed: 116 average time/residue: 0.2294 time to fit residues: 35.9723 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 : 1.382 ------------------------------------------------------------------------------- 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 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 692 LYS 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 1097 VAL Chi-restraints excluded: chain A residue 1210 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 A1102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2834 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= 0.215 Angle : 0.553 11.753 10867 Z= 0.287 Chirality : 0.039 0.171 1160 Planarity : 0.003 0.033 1402 Dihedral : 3.717 24.280 1072 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.26 % Allowed : 24.24 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 949 helix: 1.91 (0.21), residues: 654 sheet: -0.77 (0.95), residues: 32 loop : -1.32 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 850 HIS 0.016 0.002 HIS A 423 PHE 0.018 0.002 PHE A 759 TYR 0.017 0.001 TYR A 755 ARG 0.003 0.000 ARG A1006 *********************** 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 122 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6885 (tt0) REVERT: A 267 GLU cc_start: 0.8050 (pm20) cc_final: 0.7824 (mp0) REVERT: A 396 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.5766 (pm20) REVERT: A 692 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6831 (mptt) REVERT: A 760 ILE cc_start: 0.7887 (tp) cc_final: 0.7642 (tt) REVERT: A 904 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8357 (pptt) REVERT: A 1043 ASP cc_start: 0.7566 (m-30) cc_final: 0.7218 (m-30) REVERT: A 1097 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8235 (m) REVERT: A 1224 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6788 (ttm110) outliers start: 28 outliers final: 17 residues processed: 114 average time/residue: 0.2215 time to fit residues: 34.0951 Evaluate side-chains 103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 396 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 692 LYS 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 1097 VAL Chi-restraints excluded: chain A residue 1102 ASN 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 10 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 A1102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2988 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= 0.144 Angle : 0.532 11.596 10867 Z= 0.272 Chirality : 0.037 0.148 1160 Planarity : 0.003 0.034 1402 Dihedral : 3.559 25.072 1072 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.50 % Allowed : 23.66 % 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: 1.70 (0.29), residues: 949 helix: 2.14 (0.21), residues: 649 sheet: -0.57 (0.96), residues: 32 loop : -1.25 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 954 HIS 0.005 0.001 HIS A 500 PHE 0.017 0.001 PHE A 759 TYR 0.014 0.001 TYR A 755 ARG 0.004 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 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7007 (tt0) REVERT: A 692 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6758 (mptt) REVERT: A 760 ILE cc_start: 0.7754 (tp) cc_final: 0.7473 (tt) REVERT: A 875 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 1043 ASP cc_start: 0.7569 (m-30) cc_final: 0.7191 (m-30) REVERT: A 1097 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8098 (m) REVERT: A 1224 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6715 (ttm110) outliers start: 30 outliers final: 18 residues processed: 113 average time/residue: 0.1955 time to fit residues: 30.8431 Evaluate side-chains 101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 365 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU 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 54 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8092 Z= 0.278 Angle : 0.593 11.017 10867 Z= 0.306 Chirality : 0.040 0.193 1160 Planarity : 0.004 0.032 1402 Dihedral : 3.811 25.379 1072 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.08 % Allowed : 23.31 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 949 helix: 1.95 (0.21), residues: 646 sheet: -0.97 (0.92), residues: 33 loop : -1.24 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 887 HIS 0.017 0.002 HIS A 496 PHE 0.018 0.002 PHE A 759 TYR 0.019 0.002 TYR A 755 ARG 0.004 0.000 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7860 (ptp-110) REVERT: A 396 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.5715 (pm20) REVERT: A 661 ARG cc_start: 0.7167 (ttm170) cc_final: 0.6832 (ttm-80) REVERT: A 692 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6805 (mptt) REVERT: A 760 ILE cc_start: 0.7837 (tp) cc_final: 0.7570 (tt) REVERT: A 875 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 904 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8353 (pptt) REVERT: A 1043 ASP cc_start: 0.7539 (m-30) cc_final: 0.7198 (m-30) REVERT: A 1097 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8308 (m) outliers start: 35 outliers final: 23 residues processed: 110 average time/residue: 0.1958 time to fit residues: 30.2864 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 422 THR 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 692 LYS Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1210 GLU Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1220 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 423 HIS A 496 HIS A1102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.002 0.038 8092 Z= 0.153 Angle : 0.543 10.995 10867 Z= 0.280 Chirality : 0.038 0.166 1160 Planarity : 0.003 0.034 1402 Dihedral : 3.648 26.062 1072 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.50 % Allowed : 23.89 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.29), residues: 949 helix: 2.11 (0.21), residues: 649 sheet: -0.59 (0.93), residues: 32 loop : -1.26 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 954 HIS 0.019 0.002 HIS A 496 PHE 0.016 0.001 PHE A 759 TYR 0.016 0.001 TYR A 755 ARG 0.003 0.000 ARG A 787 *********************** 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 115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7107 (ttm170) cc_final: 0.6782 (ttm-80) REVERT: A 692 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6774 (mptt) REVERT: A 760 ILE cc_start: 0.7793 (tp) cc_final: 0.7504 (tt) REVERT: A 875 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 1043 ASP cc_start: 0.7569 (m-30) cc_final: 0.7209 (m-30) REVERT: A 1097 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8140 (m) outliers start: 30 outliers final: 22 residues processed: 104 average time/residue: 0.1918 time to fit residues: 28.4297 Evaluate side-chains 106 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 365 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 496 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 692 LYS Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 942 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1108 LEU 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 42 optimal weight: 4.9990 chunk 62 optimal weight: 0.0970 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 80 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 496 HIS A 912 GLN A1102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3308 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= 0.140 Angle : 0.537 10.966 10867 Z= 0.275 Chirality : 0.037 0.141 1160 Planarity : 0.003 0.034 1402 Dihedral : 3.493 24.055 1072 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.15 % Allowed : 24.01 % 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: 1.76 (0.29), residues: 949 helix: 2.19 (0.21), residues: 649 sheet: -0.56 (0.94), residues: 32 loop : -1.24 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 954 HIS 0.015 0.001 HIS A 496 PHE 0.014 0.001 PHE A 759 TYR 0.015 0.001 TYR A 755 ARG 0.003 0.000 ARG A 787 ********************** 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 114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 661 ARG cc_start: 0.7142 (ttm170) cc_final: 0.6788 (ttm-80) REVERT: A 903 MET cc_start: 0.7495 (tpp) cc_final: 0.6316 (mtt) REVERT: A 1043 ASP cc_start: 0.7539 (m-30) cc_final: 0.7183 (m-30) REVERT: A 1097 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 1224 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6743 (ttm110) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 0.1969 time to fit residues: 29.2945 Evaluate side-chains 104 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 365 LEU Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 496 HIS Chi-restraints excluded: chain A residue 498 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 692 LYS 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 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 69 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 423 HIS A 496 HIS A1102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130876 restraints weight = 10951.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128884 restraints weight = 8855.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129813 restraints weight = 9797.518| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3341 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= 0.170 Angle : 0.551 10.971 10867 Z= 0.283 Chirality : 0.038 0.155 1160 Planarity : 0.003 0.038 1402 Dihedral : 3.516 23.886 1072 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.56 % Allowed : 24.94 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.29), residues: 949 helix: 2.17 (0.21), residues: 649 sheet: -0.57 (0.94), residues: 32 loop : -1.22 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 959 HIS 0.017 0.001 HIS A 496 PHE 0.020 0.001 PHE A 620 TYR 0.016 0.001 TYR A 755 ARG 0.007 0.000 ARG A1173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1704.71 seconds wall clock time: 31 minutes 59.66 seconds (1919.66 seconds total)